Global transcriptional changes across multiple isogenic C9orf72 patient iPSC-derived neurons.

Code ↔ Paper

The paper beside its authors' code: matches between them have not been computed for this paper yet.

Paper

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The authors' code

Shell · 10 lines · 295 B · MIT

# usage:
# extractSJfromGTF.sh in.gtf > out.sj
#
# assumes transcript_id in the 12th field of GTF
#
awk '$3=="exon" {print $12,$1,$4,$5,$7}' $1 |\
sort -k1,1V -k2,2V -k3,3n |\
awk 'BEGIN {OFS="\t"} {if (t==$1) {print $2,e1+1,$3-1,$5}; e1=$4;t=$1 }' |\
sort -k1,1V -k2,2n -k3,3n -k4,4 | uniq

extractSJfromGTF.sh at commit b1edc12, under MIT · at the source

Overview

Authors: Aparna Sreeram^1,2, Desiree M Baron¹, Alberto Brusati¹, Karly Stallworth¹, Jack Humphrey^3,4,5,6, John E Landers¹

ORCID iDs: Aparna Sreeram

Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
Program in Neuroscience, Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA

Institutions: University of Massachusetts Chan Medical School (United States); Icahn School of Medicine at Mount Sinai (United States)

Journal: iScience, volume 29, issue 6, article 116054

Dates: received 5 November 2025; accepted 5 May 2026; published online 22 May 2026

Type: Research article · Language: English

License: CC BY-NC-ND

Identifiers: DOI 10.1016/j.isci.2026.116054 · PMID 42221822 · PMCID PMC13217883 · OpenAlex W7162131422

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: genetics / omics (modality), human (organism), cellular / molecular (subfield)

Methods: Spectral & time-frequency, Statistics, Smoothing, state filtering, decompositions

Keywords: Genomics, Neuroscience, Cell biology

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

Funding: National Institutes of Health

Citations: cited by 2 papers (Europe PMC); 67 references in the paper

Research resources: Anti-GAPDH Antibody RRID:AB_10077604, Human Oct4 Antibody RRID:AB_10719296, Donkey Anti-Rabbit IgG 594 RRID:AB_141637, Goat Anti-Rabbit 488 RRID:AB_143165, Mouse Anti-Cathepsin F RRID:AB_2087381, Rabbit anti-Lamin B1 RRID:AB_2136290, MAP2 Polyclonal Antibody RRID:AB_2137880, Chicken anti-βIII-Tubulin RRID:AB_2313564, Donkey Anti-Mouse 488 RRID:AB_2340846, Mouse anti-cleaved Caspase-3 RRID:AB_2341188, Donkey Anti-Mouse 546 RRID:AB_2534012, RRID:AB_2563610, Rabbit Anti-RAN Antibody RRID:AB_2620172, Mouse anti-FLNB RRID:AB_2735183, Rabbit anti-VGLUT1 RRID:AB_2881348, Mouse anti-Tau1 RRID:AB_3068606, RRID:AB_3657808, Rabbit Anti-TDP-43 RRID:AB_615042, CS29iALS-C9n1 (C929 mutant iPSC) RRID:CVCL_W559, CS52iALS-C9n1 (C952 mutant iPSC) RRID:CVCL_W561

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above.

alexdobin/STAR

License: MIT

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: b1edc1208d91a53bf40ebae8669f71d50b994851, 25 January 2024

Languages: C++ (160), C/C++ (133), C (34), Shell (1), MATLAB (1)

Size: 389 files, 329 scripts

Software Heritage: not archived

Found in: the resources table

Holds: README, license file, environment (extras/docker/Dockerfile), continuous integration, documentation

Not found: CITATION.cff, tests

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

331 files

extras/scripts/extractSJfromGTF.sh, Shell, 10 lines
extras/scripts/sjMotif.m, MATLAB, 45 lines
source/AlignVsTranscript.h, C/C++, 9 lines
source/BAMbinSortByCoordinate.cpp, C++, 81 lines
source/BAMbinSortByCoordinate.h, C/C++, 12 lines
source/BAMbinSortUnmapped.cpp, C++, 91 lines
source/BAMbinSortUnmapped.h, C/C++, 12 lines
source/BAMfunctions.cpp, C++, 194 lines
source/BAMfunctions.h, C/C++, 79 lines
source/BAMoutput.cpp, C++, 186 lines
source/BAMoutput.h, C/C++, 37 lines
source/Chain.cpp, C++, 126 lines
source/Chain.h, C/C++, 30 lines
source/ChimericAlign.cpp, C++, 32 lines
source/ChimericAlign.h, C/C++, 41 lines
source/ChimericAlign_chimericBAMoutput.cpp, C++, 105 lines
source/ChimericAlign_chimericJunctionOutput.cpp, C++, 23 lines
source/ChimericAlign_chimericStitching.cpp, C++, 181 lines
source/ChimericDetection.cpp, C++, 6 lines
source/ChimericDetection.h, C/C++, 29 lines
source/ChimericDetection_chimericDetectionMult.cpp, C++, 138 lines
source/ChimericSegment.cpp, C++, 32 lines
source/ChimericSegment.h, C/C++, 23 lines
source/ChimericTranscript.h, C/C++, 19 lines
source/ClipCR4.cpp, C++, 109 lines
source/ClipCR4.h, C/C++, 41 lines
source/ClipMate.h, C/C++, 34 lines
source/ClipMate_clip.cpp, C++, 78 lines
source/ClipMate_clipChunk.cpp, C++, 62 lines
source/ClipMate_initialize.cpp, C++, 32 lines
source/ErrorWarning.cpp, C++, 37 lines
source/ErrorWarning.h, C/C++, 9 lines
source/GTF.cpp, C++, 171 lines
source/GTF.h, C/C++, 36 lines
source/GTF_superTranscript.cpp, C++, 257 lines
source/GTF_transcriptGeneSJ.cpp, C++, 183 lines
source/Genome.cpp, C++, 234 lines
source/Genome.h, C/C++, 107 lines
source/Genome_genomeGenerate.cpp, C++, 438 lines
source/Genome_genomeLoad.cpp, C++, 521 lines
source/Genome_genomeOutLoad.cpp, C++, 58 lines
source/Genome_insertSequences.cpp, C++, 33 lines
source/Genome_transformGenome.cpp, C++, 324 lines
source/GlobalVariables.cpp, C++, 4 lines
source/GlobalVariables.h, C/C++, 9 lines
source/InOutStreams.cpp, C++, 44 lines
source/InOutStreams.h, C/C++, 23 lines
source/IncludeDefine.h, C/C++, 255 lines
source/OutSJ.cpp, C++, 123 lines
source/OutSJ.h, C/C++, 59 lines
source/PackedArray.cpp, C++, 43 lines
source/PackedArray.h, C/C++, 34 lines
source/ParameterInfo.h, C/C++, 112 lines
source/Parameters.cpp, C++, 1,269 lines
source/Parameters.h, C/C++, 374 lines
source/ParametersChimeric.h, C/C++, 41 lines
source/ParametersChimeric_initialize.cpp, C++, 118 lines
source/ParametersClip.h, C/C++, 37 lines
source/ParametersClip_initialize.cpp, C++, 107 lines
source/ParametersGenome.cpp, C++, 59 lines
source/ParametersGenome.h, C/C++, 63 lines
source/ParametersSolo.cpp, C++, 721 lines
source/ParametersSolo.h, C/C++, 220 lines
source/Parameters_closeReadsFiles.cpp, C++, 12 lines
source/Parameters_openReadsFiles.cpp, C++, 111 lines
source/Parameters_readFilesInit.cpp, C++, 167 lines
source/Parameters_readSAMheader.cpp, C++, 44 lines
source/Parameters_samAttributes.cpp, C++, 263 lines
source/Quantifications.cpp, C++, 37 lines
source/Quantifications.h, C/C++, 22 lines
source/ReadAlign.cpp, C++, 125 lines
source/ReadAlign.h, C/C++, 239 lines
source/ReadAlignChunk.cpp, C++, 170 lines
source/ReadAlignChunk.h, C/C++, 49 lines
source/ReadAlignChunk_mapChunk.cpp, C++, 128 lines
source/ReadAlignChunk_processChunks.cpp, C++, 302 lines
source/ReadAlign_CIGAR.cpp, C++, 62 lines
source/ReadAlign_alignBAM.cpp, C++, 614 lines
source/ReadAlign_assignAlignToWindow.cpp, C++, 130 lines
source/ReadAlign_calcCIGAR.cpp, C++, 58 lines
source/ReadAlign_chimericDetection.cpp, C++, 57 lines
source/ReadAlign_chimericDetectionOld.cpp, C++, 312 lines
source/ReadAlign_chimericDetectionOldOutput.cpp, C++, 74 lines
source/ReadAlign_chimericDetectionPEmerged.cpp, C++, 39 lines
source/ReadAlign_createExtendWindowsWithAlign.cpp, C++, 85 lines
source/ReadAlign_mapOneRead.cpp, C++, 118 lines
source/ReadAlign_mapOneReadSpliceGraph.cpp, C++, 40 lines
source/ReadAlign_mappedFilter.cpp, C++, 21 lines
source/ReadAlign_maxMappableLength2strands.cpp, C++, 115 lines
source/ReadAlign_multMapSelect.cpp, C++, 95 lines
source/ReadAlign_oneRead.cpp, C++, 124 lines
source/ReadAlign_outputAlignments.cpp, C++, 325 lines
source/ReadAlign_outputSpliceGraphSAM.cpp, C++, 164 lines
source/ReadAlign_outputTranscriptCIGARp.cpp, C++, 65 lines
source/ReadAlign_outputTranscriptSAM.cpp, C++, 359 lines
source/ReadAlign_outputTranscriptSJ.cpp, C++, 56 lines
source/ReadAlign_outputVariation.cpp, C++, 13 lines
source/ReadAlign_peOverlapMergeMap.cpp, C++, 368 lines
source/ReadAlign_quantTranscriptome.cpp, C++, 91 lines
source/ReadAlign_stitchPieces.cpp, C++, 350 lines
source/ReadAlign_stitchWindowSeeds.cpp, C++, 278 lines
source/ReadAlign_storeAligns.cpp, C++, 160 lines
source/ReadAlign_transformGenome.cpp, C++, 74 lines
source/ReadAlign_waspMap.cpp, C++, 128 lines
source/ReadAnnotations.h, C/C++, 47 lines
source/STAR.cpp, C++, 313 lines
source/SequenceFuns.cpp, C++, 445 lines
source/SequenceFuns.h, C/C++, 32 lines
source/SharedMemory.cpp, C++, 291 lines
source/SharedMemory.h, C/C++, 182 lines
source/SimpleGoodTuring/sgt.h, C/C++, 300 lines
source/SjdbClass.h, C/C++, 17 lines
source/Solo.cpp, C++, 91 lines
source/Solo.h, C/C++, 30 lines
source/SoloBarcode.cpp, C++, 152 lines
source/SoloBarcode.h, C/C++, 38 lines
source/SoloBarcode_extractBarcode.cpp, C++, 34 lines
source/SoloCommon.h, C/C++, 80 lines
source/SoloFeature.cpp, C++, 65 lines
source/SoloFeature.h, C/C++, 110 lines
source/SoloFeatureTypes.h, C/C++, 12 lines
source/SoloFeature_addBAMtags.cpp, C++, 26 lines
source/SoloFeature_cellFiltering.cpp, C++, 131 lines
source/SoloFeature_collapseUMI_Graph.cpp, C++, 172 lines
source/SoloFeature_collapseUMIall.cpp, C++, 658 lines
source/SoloFeature_countCBgeneUMI.cpp, C++, 112 lines
source/SoloFeature_countSmartSeq.cpp, C++, 159 lines
source/SoloFeature_countVelocyto.cpp, C++, 166 lines
source/SoloFeature_emptyDrops_CR.cpp, C++, 231 lines
source/SoloFeature_loadRawMatrix.cpp, C++, 141 lines
source/SoloFeature_outputResults.cpp, C++, 241 lines
source/SoloFeature_processRecords.cpp, C++, 87 lines
source/SoloFeature_quantTranscript.cpp, C++, 327 lines
source/SoloFeature_redistributeReadsByCB.cpp, C++, 80 lines
source/SoloFeature_statsOutput.cpp, C++, 123 lines
source/SoloFeature_sumThreads.cpp, C++, 101 lines
source/SoloFilteredCells.h, C/C++, 33 lines
source/SoloRead.cpp, C++, 22 lines
source/SoloRead.h, C/C++, 23 lines
source/SoloReadBarcode.cpp, C++, 51 lines
source/SoloReadBarcode.h, C/C++, 46 lines
source/SoloReadBarcodeStats.h, C/C++, 27 lines
source/SoloReadBarcode_getCBandUMI.cpp, C++, 429 lines
source/SoloReadFeature.cpp, C++, 63 lines
source/SoloReadFeature.h, C/C++, 50 lines
source/SoloReadFeatureStats.h, C/C++, 49 lines
source/SoloReadFeature_inputRecords.cpp, C++, 172 lines
source/SoloReadFeature_record.cpp, C++, 276 lines
source/SoloRead_record.cpp, C++, 15 lines
source/SpliceGraph.cpp, C++, 33 lines
source/SpliceGraph.h, C/C++, 58 lines
source/SpliceGraph_findSuperTr.cpp, C++, 186 lines
source/SpliceGraph_swScoreSpliced.cpp, C++, 249 lines
source/SpliceGraph_swTraceBack.cpp, C++, 19 lines
source/Stats.cpp, C++, 156 lines
source/Stats.h, C/C++, 41 lines
source/SuffixArrayFuns.cpp, C++, 410 lines
source/SuffixArrayFuns.h, C/C++, 18 lines
source/SuperTranscriptome.cpp, C++, 92 lines
source/SuperTranscriptome.h, C/C++, 42 lines
source/ThreadControl.cpp, C++, 7 lines
source/ThreadControl.h, C/C++, 29 lines
source/TimeFunctions.cpp, C++, 20 lines
source/TimeFunctions.h, C/C++, 9 lines
source/Transcript.cpp, C++, 59 lines
source/Transcript.h, C/C++, 83 lines
source/Transcript_alignScore.cpp, C++, 60 lines
source/Transcript_convertGenomeCigar.cpp, C++, 161 lines
source/Transcript_generateCigarP.cpp, C++, 63 lines
source/Transcript_transformGenome.cpp, C++, 167 lines
source/Transcript_variationAdjust.cpp, C++, 74 lines
source/Transcript_variationOutput.cpp, C++, 6 lines
source/Transcriptome.cpp, C++, 190 lines
source/Transcriptome.h, C/C++, 63 lines
source/Transcriptome_alignExonOverlap.cpp, C++, 278 lines
source/Transcriptome_classifyAlign.cpp, C++, 267 lines
source/Transcriptome_geneCountsAddAlign.cpp, C++, 63 lines
source/Transcriptome_geneFullAlignOverlap.cpp, C++, 56 lines
source/Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp, C++, 43 lines
source/Transcriptome_quantAlign.cpp, C++, 114 lines
source/Variation.cpp, C++, 157 lines
source/Variation.h, C/C++, 53 lines
source/bamRemoveDuplicates.cpp, C++, 271 lines
source/bamRemoveDuplicates.h, C/C++, 10 lines
source/bamSortByCoordinate.cpp, C++, 97 lines
source/bamSortByCoordinate.h, C/C++, 11 lines
source/bam_cat.c, C, 143 lines
source/bam_cat.h, C/C++, 8 lines
source/binarySearch2.cpp, C++, 43 lines
source/binarySearch2.h, C/C++, 7 lines
source/blocksOverlap.cpp, C++, 41 lines
source/blocksOverlap.h, C/C++, 10 lines
source/extendAlign.cpp, C++, 93 lines
source/extendAlign.h, C/C++, 6 lines
source/funCompareUintAndSuffixes.cpp, C++, 40 lines
source/funCompareUintAndSuffixes.h, C/C++, 11 lines
source/funCompareUintAndSuffixesMemcmp.cpp, C++, 33 lines
source/funCompareUintAndSuffixesMemcmp.h, C/C++, 10 lines
source/funPrimaryAlignMark.cpp, C++, 43 lines
source/funPrimaryAlignMark.h, C/C++, 5 lines
source/genomeGenerate.h, C/C++, 4 lines
source/genomeParametersWrite.cpp, C++, 45 lines
source/genomeParametersWrite.h, C/C++, 9 lines
source/genomeSAindex.cpp, C++, 217 lines
source/genomeSAindex.h, C/C++, 11 lines
source/genomeScanFastaFiles.cpp, C++, 92 lines
source/genomeScanFastaFiles.h, C/C++, 10 lines
source/htslib/bgzf.c, C, 1,085 lines
source/htslib/bgzip.c, C, 283 lines
source/htslib/config.h, C/C++, 3 lines
source/htslib/cram/cram.h, C/C++, 66 lines
source/htslib/cram/cram_codecs.c, C, 1,764 lines
source/htslib/cram/cram_codecs.h, C/C++, 155 lines
source/htslib/cram/cram_decode.c, C, 2,138 lines
source/htslib/cram/cram_decode.h, C/C++, 112 lines
source/htslib/cram/cram_encode.c, C, 2,630 lines
source/htslib/cram/cram_encode.h, C/C++, 105 lines
source/htslib/cram/cram_index.c, C, 503 lines
source/htslib/cram/cram_index.h, C/C++, 98 lines
source/htslib/cram/cram_io.c, C, 3,652 lines
source/htslib/cram/cram_io.h, C/C++, 532 lines
source/htslib/cram/cram_samtools.c, C, 144 lines
source/htslib/cram/cram_samtools.h, C/C++, 97 lines
source/htslib/cram/cram_stats.c, C, 357 lines
source/htslib/cram/cram_stats.h, C/C++, 59 lines
source/htslib/cram/cram_structs.h, C/C++, 752 lines
source/htslib/cram/files.c, C, 76 lines
source/htslib/cram/mFILE.c, C, 634 lines
source/htslib/cram/mFILE.h, C/C++, 88 lines
source/htslib/cram/md5.c, C, 295 lines
source/htslib/cram/md5.h, C/C++, 54 lines
source/htslib/cram/misc.h, C/C++, 110 lines
source/htslib/cram/open_trace_file.c, C, 386 lines
source/htslib/cram/open_trace_file.h, C/C++, 115 lines
source/htslib/cram/os.h, C/C++, 306 lines
source/htslib/cram/pooled_alloc.c, C, 170 lines
source/htslib/cram/pooled_alloc.h, C/C++, 56 lines
source/htslib/cram/sam_header.c, C, 1,222 lines
source/htslib/cram/sam_header.h, C/C++, 452 lines
source/htslib/cram/string_alloc.c, C, 153 lines
source/htslib/cram/string_alloc.h, C/C++, 69 lines
source/htslib/cram/thread_pool.c, C, 713 lines
source/htslib/cram/thread_pool.h, C/C++, 197 lines
source/htslib/cram/vlen.c, C, 432 lines
source/htslib/cram/vlen.h, C/C++, 48 lines
source/htslib/cram/zfio.c, C, 185 lines
source/htslib/cram/zfio.h, C/C++, 54 lines
source/htslib/faidx.c, C, 421 lines
source/htslib/hfile.c, C, 526 lines
source/htslib/hfile_internal.h, C/C++, 75 lines
source/htslib/hfile_net.c, C, 99 lines
source/htslib/hts.c, C, 1,326 lines
source/htslib/htslib/bgzf.h, C/C++, 313 lines
source/htslib/htslib/faidx.h, C/C++, 112 lines
source/htslib/htslib/hfile.h, C/C++, 204 lines
source/htslib/htslib/hts.h, C/C++, 305 lines
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source/htslib/htslib/klist.h, C/C++, 121 lines
source/htslib/htslib/knetfile.h, C/C++, 75 lines
source/htslib/htslib/kseq.h, C/C++, 253 lines
source/htslib/htslib/ksort.h, C/C++, 285 lines
source/htslib/htslib/kstdint.h, C/C++, 64 lines
source/htslib/htslib/kstring.h, C/C++, 270 lines
source/htslib/htslib/sam.h, C/C++, 401 lines
source/htslib/htslib/synced_bcf_reader.h, C/C++, 255 lines
source/htslib/htslib/tbx.h, C/C++, 52 lines
source/htslib/htslib/vcf.h, C/C++, 824 lines
source/htslib/htslib/vcf_sweep.h, C/C++, 15 lines
source/htslib/htslib/vcfutils.h, C/C++, 94 lines
source/htslib/kfunc.c, C, 254 lines
source/htslib/knetfile.c, C, 622 lines
source/htslib/kstring.c, C, 229 lines
source/htslib/sam.c, C, 1,797 lines
source/htslib/synced_bcf_reader.c, C, 1,183 lines
source/htslib/tabix.c, C, 374 lines
source/htslib/tbx.c, C, 290 lines
source/htslib/vcf.c, C, 2,967 lines
source/htslib/vcf_sweep.c, C, 158 lines
source/htslib/vcfutils.c, C, 642 lines
source/insertSeqSA.cpp, C++, 319 lines
source/insertSeqSA.h, C/C++, 11 lines
source/mapThreadsSpawn.cpp, C++, 33 lines
source/mapThreadsSpawn.h, C/C++, 7 lines
source/opal/opal.cpp, C++, 1,568 lines
source/opal/opal.h, C/C++, 171 lines
source/opal/simde_avx2.h, C/C++, 5,590 lines
source/outputSJ.cpp, C++, 163 lines
source/outputSJ.h, C/C++, 4 lines
source/readBarcodeLoad.h, C/C++, 9 lines
source/readLoad.cpp, C++, 100 lines
source/readLoad.h, C/C++, 12 lines
source/samHeaders.cpp, C++, 108 lines
source/samHeaders.h, C/C++, 10 lines
source/serviceFuns.cpp, C++, 351 lines
source/signalFromBAM.cpp, C++, 209 lines
source/signalFromBAM.h, C/C++, 13 lines
source/sjAlignSplit.cpp, C++, 15 lines
source/sjAlignSplit.h, C/C++, 9 lines
source/sjdbBuildIndex.cpp, C++, 333 lines
source/sjdbBuildIndex.h, C/C++, 10 lines
source/sjdbInsertJunctions.cpp, C++, 102 lines
source/sjdbInsertJunctions.h, C/C++, 10 lines
source/sjdbLoadFromFiles.cpp, C++, 27 lines
source/sjdbLoadFromFiles.h, C/C++, 10 lines
source/sjdbLoadFromStream.cpp, C++, 29 lines
source/sjdbLoadFromStream.h, C/C++, 8 lines
source/sjdbPrepare.cpp, C++, 225 lines
source/sjdbPrepare.h, C/C++, 10 lines
source/soloInputFeatureUMI.cpp, C++, 44 lines
source/soloInputFeatureUMI.h, C/C++, 13 lines
source/sortSuffixesBucket.h, C/C++, 3 lines
source/stitchAlignToTranscript.cpp, C++, 415 lines
source/stitchAlignToTranscript.h, C/C++, 7 lines
source/stitchGapIndel.cpp, C++, 59 lines
source/stitchWindowAligns.cpp, C++, 355 lines
source/stitchWindowAligns.h, C/C++, 12 lines
source/streamFuns.cpp, C++, 149 lines
source/streamFuns.h, C/C++, 17 lines
source/stringSubstituteAll.cpp, C++, 10 lines
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source/sysRemoveDir.cpp, C++, 28 lines
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source/twoPassRunPass1.cpp, C++, 97 lines
source/twoPassRunPass1.h, C/C++, 11 lines
LICENSE, License, 21 lines
README.md, Text, 115 lines

At the source: github.com/alexdobin/STAR

The paper's code and data availability statement is in the Data section.

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:

1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
329 scripts, each with its path and the digest of its content;
no match between paragraphs and code yet;
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

Datasets cited

geo:GSE303931, at NCBI GEO; found in “Data and code availability”

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

it points to a dataset: NCBI GEO GSE303931
it says that the data are available on request
it says that the code is available on request

Read it in the paper: doi.org/10.1016/j.isci.2026.116054.

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, issue, pages, dates, 6 authors, 3 keywords, 1 funder, 67 references, 20 RRIDs.

Cite

This paper

Sreeram, A., Baron, D. M., Brusati, A., Stallworth, K., Humphrey, J., & Landers, J. E. (2026). Global transcriptional changes across multiple isogenic C9orf72 patient iPSC-derived neurons. iScience, 29(6), 116054. https://doi.org/10.1016/j.isci.2026.116054

BibTeX

@article{sreeram2026global, author = {Sreeram, Aparna and Baron, Desiree M and Brusati, Alberto and Stallworth, Karly and Humphrey, Jack and Landers, John E}, title = {{Global transcriptional changes across multiple isogenic \<i\>C9orf72\</i\> patient iPSC-derived neurons}}, journal = {iScience}, year = {2026}, month = may, volume = {29}, number = {6}, pages = {116054}, publisher = {Elsevier}, issn = {2589-0042}, doi = {10.1016/j.isci.2026.116054}, url = {https://doi.org/10.1016/j.isci.2026.116054}, pmid = {42221822}, pmcid = {PMC13217883} }

RIS

TY - JOUR AU - Sreeram, Aparna AU - Baron, Desiree M AU - Brusati, Alberto AU - Stallworth, Karly AU - Humphrey, Jack AU - Landers, John E TI - Global transcriptional changes across multiple isogenic C9orf72 patient iPSC-derived neurons T2 - iScience J2 - iScience PY - 2026 DA - 2026/05/22 VL - 29 IS - 6 SP - 116054 SN - 2589-0042 PB - Elsevier DO - 10.1016/j.isci.2026.116054 UR - https://doi.org/10.1016/j.isci.2026.116054 LA - en ER -

CSL-JSON

{ "id": "10.1016/j.isci.2026.116054", "type": "article-journal", "title": "Global transcriptional changes across multiple isogenic C9orf72 patient iPSC-derived neurons", "container-title": "iScience", "author": [ { "family": "Sreeram", "given": "Aparna" }, { "family": "Baron", "given": "Desiree M" }, { "family": "Brusati", "given": "Alberto" }, { "family": "Stallworth", "given": "Karly" }, { "family": "Humphrey", "given": "Jack" }, { "family": "Landers", "given": "John E" } ], "container-title-short": "iScience", "volume": "29", "issue": "6", "page": "116054", "DOI": "10.1016/j.isci.2026.116054", "PMID": "42221822", "PMCID": "PMC13217883", "ISSN": "2589-0042", "publisher": "Elsevier", "URL": "https://doi.org/10.1016/j.isci.2026.116054", "language": "en", "issued": { "date-parts": [ [ 2026, 5, 22 ] ] } }

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Global transcriptional changes across multiple isogenic <i>C9orf72</i> patient iPSC-derived neurons.

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