Risperidone regulates the expression of schizophrenia-related genes in the forebrain of adult male mice.

Code ↔ Paper

7 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 7 matches · 2 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted

[1] § Results › Spatial patterns of gene expression in the forebrain ↔ preprocessing/functions/umap_feature_expression_plot.R, lines 195–263 · score 0.68 · Adora2a, Ppp1r2, Drd1, Drd2, Ecel1, Gad2
[2] § Results › Spatial patterns of gene expression in the forebrain ↔ preprocessing/risperidone/ris-umap-genes.R, the whole file · a weak match · score 0.67 · Adora2a, Ppp1r2, Drd1, Drd2, Ecel1, Gad2
[3] § Methods › Cluster identification and marker validation ↔ preprocessing/functions/functions-spatial-data.R, lines 71–132 · score 0.66 · Principal component, Seurat, UMAP, neighbor, variable
[4] § Methods › Cluster identification and marker validation ↔ preprocessing/old-scripts/deseq-test-analysis.R, lines 392–476 · score 0.64 · variance stabilizing transformation, log2 fold change, Clusters
[5] § Methods › Differential gene expression analysis ↔ preprocessing/functions/statistics-functions-v2.R, lines 186–234 · score 0.57 · log2 fold change, quantile normalization, assignments, clustering resolution, transcript
[6] § Methods › Peak processing, validation, and custom reference generation ↔ preprocessing/old-scripts/reduction-peaks.R, lines 333–414 · score 0.52 · amplitude, log10, coverage, BAM, summit, ratio
[7] § Results › Enrichment analysis ↔ preprocessing/clozapine/supplementaryAnalysis_paper_03.12.2025.R, the whole file · a weak match · score 0.50 · Cacna1i, Bhlhe40, Phactr3, Homer1, Kalrn, Olig2

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The paper is loaded by your browser, with JavaScript: read it at doi.org or on Europe PMC.

The authors' code

R · 267 lines · 10 KB · no license · 1 match

The registry keeps no copy of this file: its repository has no license, so its authors keep all their rights to it. Your browser shows it from its source, with JavaScript.

It can be read at the source: preprocessing/functions/umap_feature_expression_plot.R.

Overview

Authors: Magdalena Ziemiańska¹, Mateusz Zięba², Anna Radlicka-Borysewska¹, Łukasz Szumiec¹, Sławomir Gołda¹, Małgorzata Borczyk², Marcin Piechota², Michał Korostyński², Jan Rodriguez Parkitna¹

Institutions: Maj Institute of Pharmacology (Poland); Polish Academy of Sciences (Poland)

Journal: Frontiers in molecular neuroscience, volume 19, article 1844705

Dates: received 1 April 2026; accepted 12 May 2026; published online 29 May 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.3389/fnmol.2026.1844705 · PMID 42293048 · PMCID PMC13260059 · OpenAlex W7162765275

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: genetics / omics (modality), mouse (organism), schizophrenia / psychosis (population), cellular / molecular (subfield)

Methods: Statistics, Smoothing, state filtering, decompositions, Preprocessing

Keywords: antipsychotics, forebrain, gene expression, mouse, risperidone, schizophrenia, spatial transcriptomics

Topic: Neurogenesis and neuroplasticity mechanisms (Developmental Neuroscience, Neuroscience), according to OpenAlex

Citations: not cited yet (Europe PMC); 79 references in the paper

Research resources: RRID:SCR_001575, RRID:SCR_002105, RRID:SCR_014583, 000 Sequencing System RRID:SCR_016387, RRID:SCR_018555, 100 RRID:SCR_019715, RRID:SCR_020214, RRID:SCR_023571, RRID:SCR_025848

Abstract

Introduction: Risperidone is a widely used antipsychotic that reduces psychotic symptoms through modulation of monoaminergic signaling. At the cellular level, however, its effects extend beyond receptor antagonism and induce spatially discrete transcriptional responses across forebrain structures, particularly in the basal ganglia and frontal cortex.

Methods: We applied sequencing-based spatial transcriptomics to the forebrain of male C57BL/6N mice following acute risperidone treatment (0.5 mg/kg, i.p.). Unsupervised clustering of spatial transcriptomic profiles accurately delineated cortical divisions, cortical layers, and basal ganglia subregions. Differential expression analysis within anatomically defined clusters, performed using a customized statistical framework, revealed transcriptional patterns that were highly structure-specific and distinct between cortical and basal ganglia regions.

Results: Acute risperidone treatment significantly affected 95 transcripts across 12 brain regions. The most prominent transcriptional changes were concentrated in ventral forebrain structures, including the olfactory tubercle (25 differentially expressed transcripts), diagonal band nucleus (22), corpus callosum and commissures (13), and lateral septal nucleus (9). Importantly, 18 of these 95 genes have previously been implicated in schizophrenia, including Olig2, Smpd3, and Cacna1i.

Discussion: Together, these findings indicate that acute treatment with risperidone in male mice exerts pronounced molecular effects in medial and ventral forebrain regions with high oligodendrocyte and glial cell abundance. Moreover, enrichment analysis points to a molecular convergence between risperidone-induced transcription and genetic pathways implicated in schizophrenia.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 7 matches between paragraphs and lines of code.

macs3-project/MACS

License: BSD-3-Clause

State: the link answers, verified on 28 September 2026

Evidence: files inventoried

Commit: c5443190e3edfeb301cc94acf450e2b2c026a223, 25 September 2026

Languages: Python (75), C/C++ (17), C (16), Jupyter (4), Shell (2)

Size: 365 files, 114 scripts

Software Heritage: archived

Found in: the end of the paper

Holds: README, license file, environment (pyproject.toml, requirements.txt, setup.py), tests, continuous integration, documentation, 4 notebooks

Not found: CITATION.cff

Tools: NumPy (26 files), pandas (6 files), anndata (4 files), SciPy (4 files), Matplotlib (3 files), PyTorch (1 file), Scanpy (1 file)

Availability: 1 check, the latest on 28 September 2026: the link answers

28 September 2026: the link answers

116 files

MACS3/Commands/__init__.py — Python, 1 line
MACS3/Commands/bdgbroadcall_cmd.py — Python, 59 lines
MACS3/Commands/bdgcmp_cmd.py — Python, 92 lines
MACS3/Commands/bdgdiff_cmd.py — Python, 107 lines
MACS3/Commands/bdgopt_cmd.py — Python, 64 lines
MACS3/Commands/bdgpeakcall_cmd.py — Python, 65 lines
MACS3/Commands/callpeak_cmd.py — Python, 417 lines
MACS3/Commands/callvar_cmd.py — Python, 351 lines
MACS3/Commands/cmbreps_cmd.py — Python, 51 lines
MACS3/Commands/filterdup_cmd.py — Python, 132 lines
MACS3/Commands/hmmratac_cmd.py — Python, 652 lines
MACS3/Commands/pileup_cmd.py — Python, 131 lines
MACS3/Commands/pileup_v2_cmd.py — Python, 76 lines
MACS3/Commands/predictd_cmd.py — Python, 119 lines
MACS3/Commands/randsample_cmd.py — Python, 120 lines
MACS3/Commands/refinepeak_cmd.py — Python, 120 lines
MACS3/IO/BAM.py — Python, 866 lines
MACS3/IO/BedGraphIO.py — Python, 143 lines
MACS3/IO/OutputWriter.py — Python, 301 lines
MACS3/IO/Parser.py — Python, 1,570 lines
MACS3/IO/PeakIO.py — Python, 1,577 lines
MACS3/IO/__init__.py — Python, 1 line
MACS3/Signal/BedGraph.py — Python, 2,649 lines
MACS3/Signal/CallPeakUnit.py — Python, 2,294 lines
MACS3/Signal/FixWidthTrack.py — Python, 884 lines
MACS3/Signal/HMMR_EM.py — Python, 285 lines
MACS3/Signal/HMMR_HMM.py — Python, 134 lines
MACS3/Signal/HMMR_Signal_Processing.py — Python, 276 lines
MACS3/Signal/PairedEndTrack.py — Python, 2,127 lines
MACS3/Signal/PeakDetect.py — Python, 408 lines
MACS3/Signal/PeakModel.py — Python, 513 lines
MACS3/Signal/PeakVariants.py — Python, 402 lines
MACS3/Signal/Pileup.py — Python, 991 lines
MACS3/Signal/PileupV2.py — Python, 1,218 lines
MACS3/Signal/PosReadsInfo.py — Python, 670 lines
MACS3/Signal/Prob.py — Python, 1,027 lines
MACS3/Signal/RACollection.py — Python, 906 lines
MACS3/Signal/ReadAlignment.py — Python, 540 lines
MACS3/Signal/Region.py — Python, 618 lines
MACS3/Signal/ScoreTrack.py — Python, 1,974 lines
MACS3/Signal/SignalProcessing.py — Python, 368 lines
MACS3/Signal/UnitigRACollection.py — Python, 324 lines
MACS3/Signal/VariantStat.py — Python, 549 lines
MACS3/Signal/__init__.py — Python, 1 line
MACS3/Signal/cPosValCalculation.c — C, 520 lines
MACS3/Signal/cPosValCalculation.h — C/C++, 41 lines
MACS3/Signal/swalign.c — C, 358 lines
MACS3/Signal/swalign.h — C/C++, 82 lines
MACS3/Utilities/Constants.py — Python, 14 lines
MACS3/Utilities/Logger.py — Python, 34 lines
MACS3/Utilities/OptValidator.py — Python, 809 lines
MACS3/Utilities/__init__.py — Python, 1 line
MACS3/__init__.py — Python, 1 line
MACS3/fermi-lite/bfc.c — C, 683 lines
MACS3/fermi-lite/bseq.c — C, 61 lines
MACS3/fermi-lite/bubble.c — C, 366 lines
MACS3/fermi-lite/example.c — C, 50 lines
MACS3/fermi-lite/fml.h — C/C++, 197 lines
MACS3/fermi-lite/htab.c — C, 132 lines
MACS3/fermi-lite/htab.h — C/C++, 23 lines
MACS3/fermi-lite/internal.h — C/C++, 21 lines
MACS3/fermi-lite/khash.h — C/C++, 614 lines
MACS3/fermi-lite/kmer.h — C/C++, 106 lines
MACS3/fermi-lite/kseq.h — C/C++, 248 lines
MACS3/fermi-lite/ksort.h — C/C++, 309 lines
MACS3/fermi-lite/kstring.h — C/C++, 169 lines
MACS3/fermi-lite/ksw.c — C, 359 lines
MACS3/fermi-lite/ksw.h — C/C++, 71 lines
MACS3/fermi-lite/kthread.c — C, 67 lines
MACS3/fermi-lite/kvec.h — C/C++, 110 lines
MACS3/fermi-lite/mag.c — C, 620 lines
MACS3/fermi-lite/mag.h — C/C++, 69 lines
MACS3/fermi-lite/misc.c — C, 294 lines
MACS3/fermi-lite/mrope.c — C, 307 lines
MACS3/fermi-lite/mrope.h — C/C++, 114 lines
MACS3/fermi-lite/rld0.c — C, 489 lines
MACS3/fermi-lite/rld0.h — C/C++, 137 lines
MACS3/fermi-lite/rle.c — C, 191 lines
MACS3/fermi-lite/rle.h — C/C++, 78 lines
MACS3/fermi-lite/rope.c — C, 219 lines
MACS3/fermi-lite/rope.h — C/C++, 54 lines
MACS3/fermi-lite/unitig.c — C, 455 lines
docs/source/conf.py — Python, 116 lines
notebooks/10k-PBMC-test/macs3-scATAC-pbmc-10k.ipynb — Jupyter, 392 lines
notebooks/500-PBMC-test/anndata_implemetation_dev.ipynb — Jupyter, 320 lines
notebooks/500-PBMC-test/macs3-scATAC-pbmc-500-anndata.ipynb — Jupyter, 447 lines
notebooks/500-PBMC-test/macs3-scATAC-pbmc-500.ipynb — Jupyter, 367 lines
scripts/benchmark_pileup_mlx.py — Python, 270 lines
scripts/benchmark_scoretrack_torch.py — Python, 93 lines
scripts/build_docs.py — Python, 112 lines
scripts/run_macs3_release_benchmark.sh — Shell, 223 lines
scripts/run_macs_version_survey.sh — Shell, 263 lines
scripts/summarize_macs3_release_benchmark.py — Python, 218 lines
scripts/summarize_macs_version_survey.py — Python, 108 lines
setup.py — Python, 201 lines
test/jaccard.py — Python, 50 lines
test/test_BAMBAI.py — Python, 110 lines
test/test_BedGraph.py — Python, 100 lines
test/test_BedGraphIO.py — Python, 113 lines
test/test_CallPeakUnit.py — Python, 203 lines
test/test_FixWidthTrack.py — Python, 92 lines
test/test_HMMR_HMM.py — Python, 96 lines
test/test_HMMR_poisson.py — Python, 89 lines
test/test_PairedEndTrack.py — Python, 440 lines
test/test_Parser.py — Python, 48 lines
test/test_PeakDetect.py — Python, 218 lines
test/test_PeakIO.py — Python, 54 lines
test/test_PeakModel.py — Python, 145 lines
test/test_Pileup.py — Python, 452 lines
test/test_Prob.py — Python, 176 lines
test/test_Region.py — Python, 103 lines
test/test_ScoreTrack.py — Python, 300 lines
test/test_SignalProcessing.py — Python, 136 lines
test/test_online.py — Python, 42 lines
LICENSE — License, 28 lines
README.md — Text, 94 lines

At the source: github.com/macs3-project/MACS

ippas/ifpan-janrod-spatial

License: none: the authors keep all their rights

State: the link answers, verified on 28 September 2026

Evidence: files inventoried

Commit: 03f0a59895f28cd124562d4e07b397f41684a177, 1 September 2026

Languages: R (204), Python (23), Shell (8)

Size: 286 files, 235 scripts

Software Heritage: not archived

Found in: the end of the paper

Holds: README, environment (.devcontainer/devcontainer.json, preprocessing/dockerfiles/Dockerfile.peaks, preprocessing/dockerfiles/Dockerfile.r4.0.3-seurat4-package-version-spatial, preprocessing/dockerfiles/Dockerfile.r4.0.3-seurat4-package-version-spatial-update, preprocessing/dockerfiles/Dockerfile.r4.0.3-seurat4-shiny, preprocessing/dockerfiles/Dockerfile.r4.0.3-seurat4-spatial, preprocessing/dockerfiles/Dockerfile.r4.3.0-seurat5, preprocessing/dockerfiles/Dockerfile.rstudio, preprocessing/dockerfiles/Dockerfile.shiny)

Not found: license file, CITATION.cff, tests, continuous integration, documentation

Tools: tidyverse (81 files), circlize (28 files), ComplexHeatmap (28 files), pandas (21 files), patchwork (17 files), scikit-learn (15 files), Matplotlib (12 files), NumPy (12 files), edgeR (11 files), ggplot2 (11 files), anndata (6 files), Seurat (4 files), BEDTools (3 files), SciPy (3 files), igraph (2 files), limma (2 files), pysam (2 files), SAMtools (2 files), seaborn (2 files), cowplot (1 file), data.table (1 file), DESeq2 (1 file), psych (1 file), reshape2 (1 file), Scanpy (1 file)

Availability: 1 check, the latest on 28 September 2026: the link answers

28 September 2026: the link answers

236 files, not copied: shown from their source

OSCR keeps no copy of these files: this repository has no license that allows it. The reader above shows each one from its source, fetched by your browser at commit 03f0a59, when its fingerprint is the one OSCR verified. How this works.

preprocessing/bed2gtf-spaceranger.py — Python, 91 lines, shown from its source
preprocessing/clozapine/clozapine-analysis-half.R — R, 140 lines, shown from its source
preprocessing/clozapine/clozapine-analysis.R — R, 140 lines, shown from its source
preprocessing/clozapine/supplementaryAnalysis_paper_03.12.2025.R — R, 66 lines, 1 match, shown from its source
preprocessing/clozapine/umap_table_review_08.01.2026/tableXLSX_markers_ClozapineRisperidone.R — R, 223 lines, shown from its source
preprocessing/clozapine/umap_table_review_08.01.2026/tableXLSX_numberCellsPerCluster_ClozapineRisperidone.R — R, 100 lines, shown from its source
preprocessing/clozapine/umap_table_review_08.01.2026/umap_supplementary_08.01.2026.R — R, 50 lines, shown from its source
preprocessing/functions/compute_cluster_sum_mean_v3.R — R, 438 lines, shown from its source
preprocessing/functions/enrichr.R — R, 57 lines, shown from its source
preprocessing/functions/functions-shiny/selected_clusters.R — R, 15 lines, shown from its source
preprocessing/functions/functions-spatial-data.R — R, 765 lines, 1 match, shown from its source
preprocessing/functions/generate_global_heatmap/generate_global_heatmap_07.04.2026.R — R, 326 lines, shown from its source
preprocessing/functions/generate_global_heatmap/generate_global_heatmap_18.12.2025.R — R, 960 lines, shown from its source
preprocessing/functions/global-summary-espression.R — R, 119 lines, shown from its source
preprocessing/functions/heatmap-functions/plot_gene_heatmap_from_bundle.R — R, 1,274 lines, shown from its source
preprocessing/functions/heatmap-functions/plot_gene_heatmap_group_deltas_from_bundle.R — R, 223 lines, shown from its source
preprocessing/functions/heatmap-functions/plot_gene_heatmap_group_means_from_bundle.R — R, 209 lines, shown from its source
preprocessing/functions/heatmap-functions/plot_gene_heatmap_group_ratios_from_bundle.R — R, 245 lines, shown from its source
preprocessing/functions/list-genes.R — R, 308 lines, shown from its source
preprocessing/functions/permutation-test.R — R, 159 lines, shown from its source
preprocessing/functions/shiny-functions.R — R, 67 lines, shown from its source
preprocessing/functions/spatial-generate-global-heatmap.R — R, 530 lines, shown from its source
preprocessing/functions/spatial_cluster_expression_heatmap-v1.15.R — R, 169 lines, shown from its source
preprocessing/functions/spatial_cluster_select.R — R, 84 lines, shown from its source
preprocessing/functions/statistics-functions-v2.R — R, 520 lines, 1 match, shown from its source
preprocessing/functions/statistics-functions.R — R, 665 lines, shown from its source
preprocessing/functions/statistics-functions/compute_data_summary_v3.R — R, 75 lines, shown from its source
preprocessing/functions/statistics-functions/edger_pseudobuld_twofactor_generic.R — R, 181 lines, shown from its source
preprocessing/functions/statistics-functions/edger_twofactor_anova_and_posthoc.R — R, 639 lines, shown from its source
preprocessing/functions/statistics-functions/edger_twofactor_anova_and_posthoc_v2.R — R, 273 lines, shown from its source
preprocessing/functions/statistics-functions/run_edger_twoFactors_perClusters/run_edger_twoFactors_perClusters.R — R, 1,096 lines, shown from its source
preprocessing/functions/statistics-functions/run_edger_twoFactors_perClusters/run_edger_twoFactors_perClusters_v2.R — R, 1,030 lines, shown from its source
preprocessing/functions/statistics-functions/run_edger_twofactor_for_cluster.R — R, 137 lines, shown from its source
preprocessing/functions/statistics-functions/run_edger_twofactor_for_clusters_v2.R — R, 323 lines, shown from its source
preprocessing/functions/statistics-functions/statistics-function-v5.R — R, 309 lines, shown from its source
preprocessing/functions/statistics-functions/statistics-functions-v3.R — R, 754 lines, shown from its source
preprocessing/functions/statistics-functions/summarize_and_test_v2.R — R, 79 lines, shown from its source
preprocessing/functions/test-function-statistics.R — R, 214 lines, shown from its source
preprocessing/functions/umap_feature_expression_plot.R — R, 267 lines, 1 match, shown from its source
preprocessing/functions/umi-per-spot.R — R, 72 lines, shown from its source
preprocessing/functions/visualization-functions.R — R, 957 lines, shown from its source
preprocessing/functions/write_cluster_list_to_xlsx.R — R, 13 lines, shown from its source
preprocessing/functions/zero-nonzero-ratio.R — R, 168 lines, shown from its source
preprocessing/installing-require-packages.R — R, 28 lines, shown from its source
preprocessing/ldopa/ldopa-analysis.R — R, 314 lines, shown from its source
preprocessing/ldopa/ldopa-permutation-fdr.R — R, 139 lines, shown from its source
preprocessing/ldopa/test-umap-single-gene.R — R, 1 line, shown from its source
preprocessing/old-scripts/analysis-data-normalize.R — R, 143 lines, shown from its source
preprocessing/old-scripts/analysis-data-seurat.R — R, 142 lines, shown from its source
preprocessing/old-scripts/deseq-test-analysis.R — R, 477 lines, 1 match, shown from its source
preprocessing/old-scripts/generate-raport.R — R, 89 lines, shown from its source
preprocessing/old-scripts/old-code.R — R, 324 lines, shown from its source
preprocessing/old-scripts/preparation-functions.R — R, 1,041 lines, shown from its source
preprocessing/old-scripts/preparation-visualization.R — R, 117 lines, shown from its source
preprocessing/old-scripts/prepare-annotate-peaks.sh — Shell, 167 lines, shown from its source
preprocessing/old-scripts/read-data.R — R, 73 lines, shown from its source
preprocessing/old-scripts/reduction-peaks.R — R, 584 lines, 1 match, shown from its source
preprocessing/old-scripts/spaceranger-analysis.sh — Shell, 91 lines, shown from its source
preprocessing/old-scripts/statistics.R — R, 127 lines, shown from its source
preprocessing/old-scripts/visualization-seurat.R — R, 110 lines, shown from its source
preprocessing/prepare-annotate-peaks-v2.sh — Shell, 150 lines, shown from its source
preprocessing/prepare-annotate-peaks.sh — Shell, 167 lines, shown from its source
preprocessing/python/scripts/extract-coverage-for-genes-test.py — Python, 186 lines, shown from its source
preprocessing/python/src/__init__.py — Python, 1 line, shown from its source
preprocessing/python/src/bam_coverage_utils.py — Python, 152 lines, shown from its source
preprocessing/python/src/mouse_annotations_downloader.py — Python, 56 lines, shown from its source
preprocessing/python/src/plotting_functions.py — Python, 317 lines, shown from its source
preprocessing/python/src/workflow_utils.py — Python, 29 lines, shown from its source
preprocessing/pz-1190/pz-1190-analysis-half.R — R, 178 lines, shown from its source
preprocessing/pz-1190/pz-1190-analysis.R — R, 178 lines, shown from its source
preprocessing/reduction-peaks.R — R, 584 lines, shown from its source
preprocessing/risperidone-3q29/add-hoc-analysis/ris3q29-investigate-samples.R — R, 61 lines, shown from its source
preprocessing/risperidone-3q29/add-hoc-analysis/ris3q29-meanEgr3Usp48.R — R, 35 lines, shown from its source
preprocessing/risperidone-3q29/add-hoc-analysis/ris3q29-meanGenesPerSample.R — R, 50 lines, shown from its source
preprocessing/risperidone-3q29/add-hoc-analysis/ris3q29-nr3.R — R, 229 lines, shown from its source
preprocessing/risperidone-3q29/add-hoc-analysis/ris3q29-umap-25samples.R — R, 100 lines, shown from its source
preprocessing/risperidone-3q29/clustering-spatial-continuity/01_evaluateClusteringSpatialContinuity_PAS_CHAOS_ASW.R — R, 1,475 lines, shown from its source
preprocessing/risperidone-3q29/debug-summary-data-cluster4.R — R, 183 lines, shown from its source
preprocessing/risperidone-3q29/edgeR/edger_cross_cell_contrasts_by_cluster_16.06.2026.R — R, 728 lines, shown from its source
preprocessing/risperidone-3q29/edgeR/edger_cross_cell_contrasts_by_cluster_29.06.2026.R — R, 751 lines, shown from its source
preprocessing/risperidone-3q29/edgeR/investigation_logFC_edger.R — R, 29 lines, shown from its source
preprocessing/risperidone-3q29/edgeR/prepare_logCPM_per_sample_for_clusters.R — R, 351 lines, shown from its source
preprocessing/risperidone-3q29/edgeR/pseudobulk_edgeR_n25Samples_min15Spots_02.07.2026.R — R, 687 lines, shown from its source
preprocessing/risperidone-3q29/edgeR/ris3q29_edgerInteraction_test.R — R, 301 lines, shown from its source
preprocessing/risperidone-3q29/edgeR/ris3q29_edgerMarginaProportional_permutationFDRInteraction.R — R, 444 lines, shown from its source
preprocessing/risperidone-3q29/edgeR/ris3q29_edger_MarginalProportional.R — R, 626 lines, shown from its source
preprocessing/risperidone-3q29/edgeR/ris3q29_edger_scatterplotLog2FC.R — R, 164 lines, shown from its source
preprocessing/risperidone-3q29/edgeR/ris3q29_prepareExpressionByClusters_29.06.2026.R — R, 594 lines, shown from its source
preprocessing/risperidone-3q29/edgeR/ris3q29_visSumQN_heatmap.R — R, 183 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func-test.R — R, 81 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func-v1.10.R — R, 147 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func-v1.11.R — R, 159 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func-v1.12.R — R, 170 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func-v1.13.R — R, 152 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func-v1.14.R — R, 188 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func-v1.3.R — R, 127 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func-v1.4.R — R, 130 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func-v1.6.R — R, 134 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func-v1.7.R — R, 136 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func-v1.8.R — R, 143 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-func1.5.R — R, 133 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-function-v1.1.R — R, 142 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-complexheatmap-function-v1.R — R, 113 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-globalHeatmap-test.R — R, 263 lines, shown from its source
preprocessing/risperidone-3q29/heatmap/ris3q29-globalSummary-v2.R — R, 321 lines, shown from its source
preprocessing/risperidone-3q29/interaction-heatmap-16.10.2025/plot_heatmap_zscoreSalineType_customDist.R — R, 442 lines, shown from its source
preprocessing/risperidone-3q29/ris3q29-analysis-seurat-v2.R — R, 295 lines, shown from its source
preprocessing/risperidone-3q29/ris3q29-analysis-seurat.R — R, 333 lines, shown from its source
preprocessing/risperidone-3q29/ris3q29-complexheatmap.R — R, 106 lines, shown from its source
preprocessing/risperidone-3q29/ris3q29-deletion-genes-heatmap.R — R, 116 lines, shown from its source
preprocessing/risperidone-3q29/ris3q29-edgerStatistics.R — R, 389 lines, shown from its source
preprocessing/risperidone-3q29/ris3q29-find-markers.R — R, 61 lines, shown from its source
preprocessing/risperidone-3q29/ris3q29-heatmap-dev2.R — R, 159 lines, shown from its source
preprocessing/risperidone-3q29/ris3q29-statistcs.R — R, 191 lines, shown from its source
preprocessing/risperidone-3q29/ris3q29-statistics-v3.R — R, 186 lines, shown from its source
preprocessing/risperidone-3q29/ris3q29-visualization-results-test.R — R, 120 lines, shown from its source
preprocessing/risperidone-3q29/ris3q29_preapreMeanExpressionPersSampleMin20spots_09.06.2026.R — R, 336 lines, shown from its source
preprocessing/risperidone-3q29/ris3q39-heatmap.R — R, 246 lines, shown from its source
preprocessing/risperidone-3q29/sandbox/sandbox-15.10.2025/heatmap-interaction-zscoreSalinePerGenotype.R — R, 104 lines, shown from its source
preprocessing/risperidone-3q29/sandbox/sandbox-15.10.2025/heatmap-test-zscore.R — R, 46 lines, shown from its source
preprocessing/risperidone-3q29/sandbox/sandbox-15.10.2025/heatmap-test-zscore_v2.R — R, 101 lines, shown from its source
preprocessing/risperidone-3q29/sandbox/sandbox-15.10.2025/heatmap-test-zscore_v3-wtwtSalienZscore.R — R, 113 lines, shown from its source
preprocessing/risperidone-3q29/sandbox/sandbox-15.10.2025/heatmap-test-zsocre-allSamplesHeatmap.R — R, 58 lines, shown from its source
preprocessing/risperidone-3q29/sandbox/sandbox-15.10.2025/plot_gene_heatmap_group_means_refZscore_from_bundle.R — R, 251 lines, shown from its source
preprocessing/risperidone-3q29/summary-statistics-debug/compute-data-summary-debug.R — R, 170 lines, shown from its source
preprocessing/risperidone-3q29/summary-statistics-debug/summarize_and_test-debug-v2.R — R, 138 lines, shown from its source
preprocessing/risperidone-3q29/summary-statistics-debug/summarize_and_test-debug.R — R, 155 lines, shown from its source
preprocessing/risperidone-3q29/summary_clusters/summarize_cluster_barcodes_per_sample.R — R, 40 lines, shown from its source
preprocessing/risperidone/customize-clusters.R — R, 139 lines, shown from its source
preprocessing/risperidone/function-statistics.R — R, 102 lines, shown from its source
preprocessing/risperidone/gene-count-per-spot.R — R, 104 lines, shown from its source
preprocessing/risperidone/generate-raport.R — R, 89 lines, shown from its source
preprocessing/risperidone/jackcraig-prepare-spatialdata.R — R, 187 lines, shown from its source
preprocessing/risperidone/ris-umap-genes.R — R, 67 lines, 1 match, shown from its source
preprocessing/risperidone/ris_permutataion_minSpot15_16.03.2026.R — R, 762 lines, shown from its source
preprocessing/risperidone/risperidone-analysis-half-seurat5.R — R, 201 lines, shown from its source
preprocessing/risperidone/risperidone-analysis.R — R, 149 lines, shown from its source
preprocessing/risperidone/risperidone-half-analysis-defaultReference_17.03.2026.R — R, 766 lines, shown from its source
preprocessing/risperidone/risperidone-half-analysis.R — R, 320 lines, shown from its source
preprocessing/risperidone/risperidone-half-statistics-spotThreshold15-11.02.2026.R — R, 188 lines, shown from its source
preprocessing/risperidone/risperidone-half-statistics.R — R, 101 lines, shown from its source
preprocessing/risperidone/risperidone-median-transcript-per-spot.R — R, 2 lines, shown from its source
preprocessing/risperidone/risperidone_findMarkers_12.02.2026.R — R, 135 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/prepareData_toSilhouette_v1_2026.R — R, 69 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_sdmbench_chaos_pas/run_sdmbench_chaos_pas_v1_27.04.2026.py — Python, 169 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_sdmbench_chaos_pas/run_sdmbench_chaos_pas_v2_27.04.2026.py — Python, 195 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_sdmbench_chaos_pas/run_sdmbench_chaos_pas_v3_27.04.2026.py — Python, 192 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_sdmbench_chaos_pas/run_sdmbench_chaos_pas_v4_27.04.2026.py — Python, 229 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_sdmbench_chaos_pas/run_sdmbench_chaos_pas_v5_27.04.2026.py — Python, 265 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_sdmbench_chaos_pas/run_sdmbench_chaos_pas_v6_27.04.2026.py — Python, 230 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_silhouette_analysis/run_resolution_compare_0.4_vs_0.85_FAST_v1_27.04.2026.py — Python, 439 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_silhouette_analysis/run_silhouette_analysis_v1_27.04.2026.py — Python, 128 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_silhouette_analysis/run_silhouette_analysis_v2_27.04.2026.py — Python, 148 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_silhouette_analysis/run_silhouette_analysis_v3_27.04.2026.py — Python, 152 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_silhouette_analysis/run_silhouette_analysis_v4_27.04.2026.py — Python, 160 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_silhouette_analysis/run_silhouette_analysis_v5_27.04.2026.py — Python, 166 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_silhouette_analysis/run_silhouette_analysis_v6_27.04.2026.py — Python, 255 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_silhouette_analysis/run_silhouette_analysis_v7_27.04.2026.py — Python, 221 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_silhouette_analysis/run_silhouette_analysis_v8_27.04.2026.py — Python, 267 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/run_silhouette_analysis/run_silhouette_analysis_v9_27.04.2026.py — Python, 322 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/sandbox/ris-spatial-cluster-stability_v1_27.04.2026.R — R, 121 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/sandbox/ris-spatial-cluster-stability_v2_27.04.2026.R — R, 38 lines, shown from its source
preprocessing/risperidone/spatial-cluster-stability/sandbox/ris-spatial-cluster-stability_v3_08.05.2026.R — R, 101 lines, shown from its source
preprocessing/shiny-app/clusters-testing.R — R, 66 lines, shown from its source
preprocessing/shiny-app/debugging-shiny-external.R — R, 46 lines, shown from its source
preprocessing/shiny-app/debugging-shiny-inner.R — R, 45 lines, shown from its source
preprocessing/shiny-app/shiny-app-plot-test1.R — R, 94 lines, shown from its source
preprocessing/shiny-app/shiny-app-plot-test2.R — R, 64 lines, shown from its source
preprocessing/shiny-app/shiny-app-plot-test3.R — R, 48 lines, shown from its source
preprocessing/shiny-app/shiny-app-plot-test4.R — R, 78 lines, shown from its source
preprocessing/shiny-app/shiny-app-spatial5.R — R, 326 lines, shown from its source
preprocessing/shiny-app/shiny-app-spatial6.R — R, 319 lines, shown from its source
preprocessing/shiny-app/shiny-app-spatial7.R — R, 384 lines, shown from its source
preprocessing/shiny-app/shiny-app-spatial8.R — R, 539 lines, shown from its source
preprocessing/shiny-app/shiny-app-spatial9.R — R, 660 lines, shown from its source
preprocessing/shiny-app/shiny-app-test1.R — R, 79 lines, shown from its source
preprocessing/shiny-app/shiny-app-test2.R — R, 118 lines, shown from its source
preprocessing/shiny-app/shiny-app-test3.R — R, 232 lines, shown from its source
preprocessing/shiny-app/shiny-app-test4.R — R, 296 lines, shown from its source
preprocessing/shiny-app/shiny-spatial-external1.R — R, 312 lines, shown from its source
preprocessing/shiny-app/shiny-spatial-external2.R — R, 380 lines, shown from its source
preprocessing/shiny-app/shiny-spatial-external3.R — R, 523 lines, shown from its source
preprocessing/shiny-app/shiny-test-docker1.R — R, 32 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/spatial-browser-v2.0.1.R — R, 84 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/spatial-browser-v2.0.10.R — R, 923 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/spatial-browser-v2.0.11.R — R, 997 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/spatial-browser-v2.0.2.R — R, 163 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/spatial-browser-v2.0.3.R — R, 175 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/spatial-browser-v2.0.4.R — R, 218 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/spatial-browser-v2.0.5.R — R, 448 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/spatial-browser-v2.0.6.R — R, 457 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/spatial-browser-v2.0.8.R — R, 896 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/spatial-browser-v2.0.9.R — R, 671 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/spatial-browser-v2.1.0.R — R, 1,189 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.0-dev/sptial-browser-v2.0.7.R — R, 815 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.1-deploy/app.R — R, 12 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.1-deploy/global.R — R, 71 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.1-deploy/server.R — R, 589 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.1-deploy/ui.R — R, 360 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.2-deploy/app.R — R, 12 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.2-deploy/global.R — R, 158 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.2-deploy/server.R — R, 752 lines, shown from its source
preprocessing/shiny-app/spatial-browser-v2.2-deploy/ui.R — R, 421 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser1/app.R — R, 12 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser1/global.R — R, 16 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser1/server.R — R, 395 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser1/ui.R — R, 146 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser2/app.R — R, 12 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser2/global.R — R, 17 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser2/server.R — R, 455 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser2/ui.R — R, 178 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser3/app.R — R, 12 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser3/global.R — R, 18 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser3/server.R — R, 530 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser3/ui.R — R, 189 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser4/app.R — R, 12 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser4/global.R — R, 20 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser4/server.R — R, 554 lines, shown from its source
preprocessing/shiny-app/spatial-transcriptomics-drug-browser4/ui.R — R, 206 lines, shown from its source
preprocessing/spaceranger-analysis-v1.1.sh — Shell, 158 lines, shown from its source
preprocessing/spaceranger-analysis-v2.sh — Shell, 102 lines, shown from its source
preprocessing/spaceranger-analysis.sh — Shell, 103 lines, shown from its source
preprocessing/spaceranger-analysis2.sh — Shell, 106 lines, shown from its source
preprocessing/tested-scripts/development-statistics.R — R, 283 lines, shown from its source
preprocessing/tested-scripts/development-statistics2.R — R, 230 lines, shown from its source
preprocessing/tested-scripts/edger--statistics.R — R, 59 lines, shown from its source
preprocessing/tested-scripts/multiple-generating-png.R — R, 307 lines, shown from its source
preprocessing/tested-scripts/quartile-normalization-test.R — R, 250 lines, shown from its source
preprocessing/tested-scripts/statistics.R — R, 238 lines, shown from its source
preprocessing/tested-scripts/test.r — R, 55 lines, shown from its source
preprocessing/tested-scripts/visualization-seurat.R — R, 110 lines, shown from its source
preprocessing/to-remove/analysis-data-normalize.R — R, 143 lines, shown from its source
preprocessing/to-remove/analysis-data-seurat.R — R, 118 lines, shown from its source
preprocessing/to-remove/preparation-visualization.R — R, 137 lines, shown from its source
preprocessing/to-remove/read-data.R — R, 73 lines, shown from its source
README.md — Text, 91 lines, shown from its source

At the source: github.com/ippas/ifpan-janrod-spatial

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
349 scripts, each with its path and the digest of its content;
7 matches between paragraphs of the paper and lines of the code (method lexical-v1);
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability statement

The RNAseq dataset generated for this study can be found in the Sequence Read Archive, https://www.ncbi.nlm.nih.gov/, under accession number PRJNA1143882.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 9 authors, 7 keywords, 79 references, 9 RRIDs.

Cite

This paper

Ziemiańska, M., Zięba, M., Radlicka-Borysewska, A., Szumiec, Ł., Gołda, S., Borczyk, M., Piechota, M., Korostyński, M., & Rodriguez Parkitna, J. (2026). Risperidone regulates the expression of schizophrenia-related genes in the forebrain of adult male mice. Frontiers in molecular neuroscience, 19, 1844705. https://doi.org/10.3389/fnmol.2026.1844705

BibTeX

@article{ziemianska2026risperidone, author = {Ziemiańska, Magdalena and Zięba, Mateusz and Radlicka-Borysewska, Anna and Szumiec, Łukasz and Gołda, Sławomir and Borczyk, Małgorzata and Piechota, Marcin and Korostyński, Michał and Rodriguez Parkitna, Jan}, title = {{Risperidone regulates the expression of schizophrenia-related genes in the forebrain of adult male mice}}, journal = {Frontiers in molecular neuroscience}, year = {2026}, month = may, volume = {19}, pages = {1844705}, publisher = {Frontiers Media SA}, issn = {1662-5099}, doi = {10.3389/fnmol.2026.1844705}, url = {https://doi.org/10.3389/fnmol.2026.1844705}, pmid = {42293048}, pmcid = {PMC13260059} }

RIS

TY - JOUR AU - Ziemiańska, Magdalena AU - Zięba, Mateusz AU - Radlicka-Borysewska, Anna AU - Szumiec, Łukasz AU - Gołda, Sławomir AU - Borczyk, Małgorzata AU - Piechota, Marcin AU - Korostyński, Michał AU - Rodriguez Parkitna, Jan TI - Risperidone regulates the expression of schizophrenia-related genes in the forebrain of adult male mice T2 - Frontiers in molecular neuroscience J2 - Front Mol Neurosci PY - 2026 DA - 2026/05/29 VL - 19 SP - 1844705 SN - 1662-5099 PB - Frontiers Media SA DO - 10.3389/fnmol.2026.1844705 UR - https://doi.org/10.3389/fnmol.2026.1844705 LA - en ER -

CSL-JSON

{ "id": "10.3389/fnmol.2026.1844705", "type": "article-journal", "title": "Risperidone regulates the expression of schizophrenia-related genes in the forebrain of adult male mice", "container-title": "Frontiers in molecular neuroscience", "author": [ { "family": "Ziemiańska", "given": "Magdalena" }, { "family": "Zięba", "given": "Mateusz" }, { "family": "Radlicka-Borysewska", "given": "Anna" }, { "family": "Szumiec", "given": "Łukasz" }, { "family": "Gołda", "given": "Sławomir" }, { "family": "Borczyk", "given": "Małgorzata" }, { "family": "Piechota", "given": "Marcin" }, { "family": "Korostyński", "given": "Michał" }, { "family": "Rodriguez Parkitna", "given": "Jan" } ], "container-title-short": "Front Mol Neurosci", "volume": "19", "page": "1844705", "DOI": "10.3389/fnmol.2026.1844705", "PMID": "42293048", "PMCID": "PMC13260059", "ISSN": "1662-5099", "publisher": "Frontiers Media SA", "URL": "https://doi.org/10.3389/fnmol.2026.1844705", "language": "en", "issued": { "date-parts": [ [ 2026, 5, 29 ] ] } }

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1002/imt2.70163 [code]: Spatial multi-omics unveils sphingolipid metabolic reprogramming within the retinal pathological niche.
Journal: iMeta
In common: edgeR, limma, anndata, 18 other tools, genetics / omics, mouse, cellular / molecular, 1 reference
[2] doi:10.1038/s41467-026-76675-1 [code]: Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.
Journal: Nature communications
In common: pysam, BEDTools, SAMtools, 18 other tools, genetics / omics
[3] doi:10.1038/s41593-026-02300-5 [code]: Integrated single-cell and spatial transcriptomic profiling in ALS uncovers peripheral-to-central immune infiltration and reprogramming.
Journal: Nature neuroscience
In common: SAMtools, edgeR, anndata, 18 other tools, genetics / omics, cellular / molecular
[4] doi:10.1038/s42003-026-10957-8 [code]: Brain defence by the extracellular matrix protein Cochlin.
Journal: Communications biology
In common: SAMtools, edgeR, limma, 17 other tools, mouse, cellular / molecular, 1 reference
[5] doi:10.1016/j.cpblue.2026.100007 [code]: An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.
Journal: Cell press blue
In common: SAMtools, edgeR, limma, 18 other tools
[6] doi:10.1186/s13059-026-04177-w [code]: Genomic sequence evolution underlying human neocortical interareal diversification.
Journal: Genome biology
In common: pysam, BEDTools, SAMtools, 16 other tools, genetics / omics, mouse, cellular / molecular
[7] doi:10.1126/sciadv.aeg3223 [code]: The extreme diversity of retinal amacrine cells has deep evolutionary roots.
Journal: Science advances
In common: psych, anndata, DESeq2, 17 other tools, genetics / omics, cellular / molecular
[8] doi:10.1038/s41586-026-10512-9 [code]: Astrocyte glucocorticoid receptor signalling restricts neuronal plasticity.
Journal: Nature
In common: pysam, BEDTools, SAMtools, 14 other tools, mouse, cellular / molecular, 1 reference
[9] doi:10.1093/bioinformatics/btag592 [code]: Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease.
Journal: Bioinformatics (Oxford, England)
In common: SAMtools, edgeR, limma, 16 other tools, genetics / omics
[10] doi:10.1038/s44318-026-00818-9 [code]: FAM134B-mediated ER-phagy degrades APP and suppresses Alzheimer's disease pathology.
Journal: The EMBO journal
In common: BEDTools, limma, anndata, 16 other tools, mouse, cellular / molecular

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.