Tools
233 tools found in the authors' code of the papers with a page, the most used first. The tools are read from the scripts of the authors' repositories (what the scripts import).
- NumPy (library), 11,089 papers, 13,416 repositories
- Matplotlib (library), 9,057 papers, 10,633 repositories
- SciPy (library), 8,621 papers, 9,938 repositories
- pandas (library), 8,490 papers, 9,954 repositories
- scikit-learn (library), 5,729 papers, 6,307 repositories
- tidyverse (library), 5,029 papers, 5,807 repositories
- Statistics and Machine Learning Toolbox (toolbox), 4,907 papers, 5,052 repositories
- seaborn (library), 4,701 papers, 5,220 repositories
- ggplot2 (library), 4,273 papers, 4,882 repositories
- PyTorch (library), 3,074 papers, 3,431 repositories
- Image Processing Toolbox (toolbox), 2,388 papers, 2,161 repositories
- NiBabel (library), 2,322 papers, 2,101 repositories
- Signal Processing Toolbox (toolbox), 2,246 papers, 2,247 repositories
- statsmodels (library), 2,175 papers, 2,214 repositories
- Pillow (library), 1,872 papers, 1,887 repositories
- data.table (library), 1,814 papers, 2,000 repositories
- ggpubr (library), 1,810 papers, 2,014 repositories
- reshape2 (library), 1,785 papers, 1,980 repositories
- h5py (library), 1,750 papers, 1,809 repositories
- scikit-image (library), 1,636 papers, 1,711 repositories
- cowplot (library), 1,501 papers, 1,639 repositories
- SPM (toolbox), 1,460 papers, 1,104 repositories
- patchwork (library), 1,457 papers, 1,623 repositories
- TensorFlow (library), 1,385 papers, 1,411 repositories
- OpenCV (library), 1,369 papers, 1,509 repositories
- lme4 (library), 1,270 papers, 1,352 repositories
- FSL (software), 1,269 papers, 973 repositories
- Seurat (library), 1,266 papers, 1,564 repositories
- Plotly (library), 1,146 papers, 1,153 repositories
- NetworkX (library), 1,105 papers, 1,141 repositories
- FreeSurfer (software), 1,095 papers, 741 repositories
- Nilearn (library), 1,092 papers, 1,004 repositories
- Parallel Computing Toolbox (toolbox), 1,089 papers, 929 repositories
- pheatmap (library), 1,026 papers, 1,167 repositories
- Keras (library), 1,017 papers, 1,050 repositories
- Optimization Toolbox (toolbox), 986 papers, 830 repositories
- lmerTest (library), 967 papers, 1,013 repositories
- FieldTrip (toolbox), 897 papers, 741 repositories
- MNE-Python (library), 858 papers, 934 repositories
- Numba (library), 833 papers, 766 repositories
- igraph (library), 805 papers, 807 repositories
- UMAP (library), 769 papers, 752 repositories
- DESeq2 (library), 759 papers, 851 repositories
- car (library), 735 papers, 762 repositories
- ComplexHeatmap (library), 734 papers, 869 repositories
- emmeans (library), 734 papers, 795 repositories
- ANTs (software), 727 papers, 489 repositories
- EEGLAB (toolbox), 710 papers, 691 repositories
- Scanpy (library), 701 papers, 891 repositories
- psych (library), 688 papers, 684 repositories
- clusterProfiler (library), 676 papers, 784 repositories
- rstatix (library), 640 papers, 690 repositories
- circlize (library), 624 papers, 724 repositories
- easystats (library), 616 papers, 655 repositories
- Tools for NIfTI and ANALYZE image (MATLAB) (toolbox), 604 papers, 397 repositories
- limma (library), 600 papers, 611 repositories
- broom (library), 598 papers, 640 repositories
- anndata (library), 563 papers, 696 repositories
- tifffile (library), 525 papers, 570 repositories
- SAMtools (software), 505 papers, 535 repositories
- GIfTI library for MATLAB (toolbox), 501 papers, 277 repositories
- Pingouin (library), 495 papers, 525 repositories
- edgeR (library), 485 papers, 523 repositories
- SingleCellExperiment (library), 475 papers, 495 repositories
- BEDTools (software), 454 papers, 418 repositories
- Curve Fitting Toolbox (toolbox), 452 papers, 390 repositories
- AFNI (software), 451 papers, 314 repositories
- Brain Connectivity Toolbox (toolbox), 447 papers, 361 repositories
- SimpleITK (library), 440 papers, 378 repositories
- reticulate (library), 432 papers, 428 repositories
- imageio (library), 426 papers, 406 repositories
- XGBoost (library), 419 papers, 400 repositories
- shadedErrorBar (toolbox), 382 papers, 430 repositories
- Harmony (library), 372 papers, 392 repositories
- Biopython (library), 370 papers, 367 repositories
- Psychtoolbox (toolbox), 364 papers, 355 repositories
- Connectome Workbench (software), 345 papers, 181 repositories
- nlme (library), 342 papers, 341 repositories
- CircStat (toolbox), 335 papers, 348 repositories
- caret (library), 314 papers, 331 repositories
- fdr_bh (Benjamini-Hochberg FDR) (toolbox), 304 papers, 233 repositories
- SHAP (library), 290 papers, 273 repositories
- pysam (library), 286 papers, 330 repositories
- WGCNA (library), 286 papers, 304 repositories
- export_fig (toolbox), 284 papers, 227 repositories
- pydicom (library), 282 papers, 237 repositories
- Violinplot-Matlab (toolbox), 279 papers, 269 repositories
- rpy2 (library), 267 papers, 250 repositories
- Nipype (library), 266 papers, 215 repositories
- Hugging Face Transformers (library), 262 papers, 272 repositories
- PyTorch Lightning (library), 259 papers, 264 repositories
- glmnet (library), 255 papers, 245 repositories
- xarray (library), 255 papers, 258 repositories
- Monocle 3 (library), 251 papers, 276 repositories
- DIPY (library), 237 papers, 183 repositories
- MRtrix3 (software), 230 papers, 169 repositories
- survival (library), 228 papers, 236 repositories
- lavaan (library), 220 papers, 225 repositories
- statannotations (library), 220 papers, 226 repositories
- mgcv (library), 215 papers, 238 repositories
- PyTorch Geometric (library), 215 papers, 235 repositories
- BrainSpace (library), 211 papers, 163 repositories
- NEURON (software), 209 papers, 301 repositories
- Wavelet Toolbox (toolbox), 196 papers, 183 repositories
- STAR (software), 195 papers, 209 repositories
- PsychoPy (software), 194 papers, 200 repositories
- pROC (library), 189 papers, 200 repositories
- afex (library), 188 papers, 206 repositories
- boundedline (toolbox), 187 papers, 146 repositories
- Stan (software), 185 papers, 207 repositories
- JAX (library), 182 papers, 208 repositories
- MONAI (library), 180 papers, 171 repositories
- multcomp (library), 176 papers, 190 repositories
- PyBIDS (library), 175 papers, 135 repositories
- ICLabel (toolbox), 171 papers, 164 repositories
- imbalanced-learn (library), 170 papers, 168 repositories
- CuPy (library), 166 papers, 148 repositories
- neuromaps (library), 162 papers, 137 repositories
- brms (library), 161 papers, 176 repositories
- ggseg (library), 159 papers, 165 repositories
- BayesFactor (library), 152 papers, 155 repositories
- Chronux (toolbox), 152 papers, 136 repositories
- cifti-matlab (toolbox), 150 papers, 82 repositories
- scikit-posthocs (library), 149 papers, 177 repositories
- SymPy (library), 147 papers, 171 repositories
- Neurodata Without Borders (PyNWB, MatNWB) (library), 145 papers, 125 repositories
- Snakemake (software), 145 papers, 178 repositories
- BCFtools (software), 143 papers, 159 repositories
- randomForest (library), 141 papers, 111 repositories
- dcm2niix (software), 138 papers, 117 repositories
- RDKit (library), 131 papers, 137 repositories
- specparam (formerly FOOOF) (library), 131 papers, 133 repositories
- PyWavelets (library), 127 papers, 131 repositories
- napari (software), 122 papers, 132 repositories
- BrainSMASH (library), 117 papers, 75 repositories
- Brian 2 (library), 117 papers, 148 repositories
- Neo (library), 117 papers, 142 repositories
- abagen (library), 115 papers, 66 repositories
- Subread (featureCounts) (software), 115 papers, 118 repositories
- LightGBM (library), 110 papers, 104 repositories
- tedana (library), 109 papers, 24 repositories
- scVelo (library), 108 papers, 128 repositories
- FastQC (software), 107 papers, 121 repositories
- glmmTMB (library), 107 papers, 120 repositories
- ArviZ (library), 105 papers, 104 repositories
- AllenSDK (library), 104 papers, 103 repositories
- fMRIPrep (software), 103 papers, 81 repositories
- PyMC (library), 99 papers, 78 repositories
- Plots.jl (library), 96 papers, 108 repositories
- neuroCombat (library), 95 papers, 68 repositories
- DataFrames.jl (library), 94 papers, 128 repositories
- Distributions.jl (library), 94 papers, 118 repositories
- netneurotools (library), 92 papers, 88 repositories
- nnU-Net (software), 91 papers, 67 repositories
- metafor (library), 89 papers, 90 repositories
- Deep Learning Toolbox (toolbox), 88 papers, 86 repositories
- MNE-BIDS (library), 85 papers, 88 repositories
- Brainstorm (toolbox), 84 papers, 80 repositories
- RNifti (library), 76 papers, 36 repositories
- autoreject (library), 75 papers, 83 repositories
- ImageJ / Fiji (software), 75 papers, 68 repositories
- MNE-Connectivity (library), 75 papers, 70 repositories
- CAT12 (toolbox), 71 papers, 34 repositories
- Cell Ranger (software), 70 papers, 95 repositories
- CoSMoMVPA (toolbox), 68 papers, 65 repositories
- Squidpy (library), 67 papers, 87 repositories
- NEST Simulator (software), 65 papers, 89 repositories
- Kilosort (software), 64 papers, 44 repositories
- Nextflow (software), 63 papers, 62 repositories
- deepTools (software), 62 papers, 74 repositories
- PyRadiomics (library), 60 papers, 43 repositories
- ERPLAB (toolbox), 59 papers, 57 repositories
- Elephant (library), 58 papers, 77 repositories
- SpikeInterface (library), 58 papers, 59 repositories
- DataLad (software), 56 papers, 62 repositories
- Open Ephys analysis tools (library), 55 papers, 49 repositories
- Cellpose (software), 53 papers, 61 repositories
- DPABI (toolbox), 53 papers, 29 repositories
- DeepLabCut (software), 52 papers, 41 repositories
- GIFT (toolbox), 52 papers, 22 repositories
- JAGS (software), 51 papers, 40 repositories
- pyABF (library), 51 papers, 54 repositories
- BIDS Validator (software), 49 papers, 35 repositories
- CaImAn (library), 49 papers, 47 repositories
- HCP Pipelines (software), 49 papers, 29 repositories
- TemplateFlow (library), 49 papers, 38 repositories
- pycortex (library), 48 papers, 47 repositories
- OHBA Software Library (OSL) (toolbox), 45 papers, 44 repositories
- NeuroKit2 (library), 43 papers, 51 repositories
- DifferentialEquations.jl (library), 41 papers, 49 repositories
- LMFIT (library), 41 papers, 53 repositories
- NeuroDSP (library), 41 papers, 41 repositories
- pyRiemann (library), 41 papers, 45 repositories
- Phy (software), 39 papers, 24 repositories
- Makie (library), 38 papers, 57 repositories
- neuroHarmonize (library), 36 papers, 21 repositories
- Pyro (library), 36 papers, 32 repositories
- Salmon (software), 34 papers, 40 repositories
- The Virtual Brain (software), 34 papers, 32 repositories
- NiMARE (library), 33 papers, 42 repositories
- nltools (library), 33 papers, 41 repositories
- MRIQC (software), 31 papers, 23 repositories
- YASA (library), 31 papers, 32 repositories
- Dcm2Bids (software), 29 papers, 18 repositories
- HeuDiConv (software), 29 papers, 31 repositories
- Network-Based Statistic (NBS) (toolbox), 28 papers, 22 repositories
- Suite2p (software), 28 papers, 32 repositories
- MDAnalysis (library), 27 papers, 32 repositories
- LFPy (library), 26 papers, 35 repositories
- Flux.jl (library), 24 papers, 27 repositories
- Braindecode (library), 23 papers, 25 repositories
- PyPREP (library), 23 papers, 27 repositories
- BrainIAK (library), 19 papers, 21 repositories
- MOABB (library), 19 papers, 20 repositories
- permuco (library), 19 papers, 21 repositories
- GLMsingle (library), 18 papers, 17 repositories
- psignifit (library), 18 papers, 23 repositories
- CONN (toolbox), 17 papers, 17 repositories
- NetPyNE (library), 17 papers, 22 repositories
- jsPsych (library), 16 papers, 21 repositories
- eegUtils (library), 15 papers, 16 repositories
- QSIPrep (software), 15 papers, 16 repositories
- WFDB Python (library), 15 papers, 13 repositories
- Nighres (library), 14 papers, 12 repositories
- Bambi (library), 13 papers, 17 repositories
- MEEGkit (library), 12 papers, 12 repositories
- Nengo (library), 12 papers, 13 repositories
- Turing.jl (library), 11 papers, 12 repositories
- PyNN (library), 9 papers, 14 repositories
- MountainSort (software), 5 papers, 4 repositories
- SpyKING CIRCUS (software), 4 papers, 4 repositories
- bycycle (library), 3 papers, 4 repositories
- SLEAP (software), 1 paper, 1 repository