Tools
228 tools found in the authors' code of the papers with a page, the most used first. A tool is found in the scripts of the authors' repositories (what they import), not in the text of the paper.
- NumPy (library) — 1,460 papers, 1,989 repositories
- Matplotlib (library) — 1,182 papers, 1,577 repositories
- SciPy (library) — 1,161 papers, 1,540 repositories
- pandas (library) — 1,152 papers, 1,537 repositories
- scikit-learn (library) — 770 papers, 971 repositories
- tidyverse (library) — 715 papers, 895 repositories
- seaborn (library) — 617 papers, 778 repositories
- ggplot2 (library) — 594 papers, 747 repositories
- Statistics and Machine Learning Toolbox (toolbox) — 513 papers, 614 repositories
- PyTorch (library) — 481 papers, 596 repositories
- NiBabel (library) — 334 papers, 375 repositories
- statsmodels (library) — 323 papers, 374 repositories
- patchwork (library) — 255 papers, 306 repositories
- Pillow (library) — 249 papers, 295 repositories
- data.table (library) — 246 papers, 313 repositories
- Image Processing Toolbox (toolbox) — 246 papers, 268 repositories
- Signal Processing Toolbox (toolbox) — 245 papers, 294 repositories
- h5py (library) — 239 papers, 287 repositories
- ggpubr (library) — 233 papers, 279 repositories
- reshape2 (library) — 230 papers, 289 repositories
- scikit-image (library) — 216 papers, 260 repositories
- OpenCV (library) — 195 papers, 244 repositories
- cowplot (library) — 192 papers, 221 repositories
- Seurat (library) — 184 papers, 241 repositories
- lme4 (library) — 180 papers, 202 repositories
- SPM (toolbox) — 158 papers, 158 repositories
- Plotly (library) — 152 papers, 173 repositories
- Nilearn (library) — 149 papers, 158 repositories
- NetworkX (library) — 146 papers, 185 repositories
- pheatmap (library) — 146 papers, 178 repositories
- FSL (software) — 145 papers, 151 repositories
- TensorFlow (library) — 137 papers, 153 repositories
- lmerTest (library) — 134 papers, 147 repositories
- MNE-Python (library) — 131 papers, 156 repositories
- ComplexHeatmap (library) — 128 papers, 161 repositories
- FreeSurfer (software) — 124 papers, 120 repositories
- Scanpy (library) — 122 papers, 181 repositories
- emmeans (library) — 118 papers, 134 repositories
- FieldTrip (toolbox) — 118 papers, 110 repositories
- clusterProfiler (library) — 116 papers, 146 repositories
- Numba (library) — 114 papers, 127 repositories
- circlize (library) — 111 papers, 142 repositories
- Parallel Computing Toolbox (toolbox) — 110 papers, 118 repositories
- broom (library) — 108 papers, 123 repositories
- anndata (library) — 107 papers, 155 repositories
- DESeq2 (library) — 107 papers, 123 repositories
- igraph (library) — 107 papers, 130 repositories
- EEGLAB (toolbox) — 104 papers, 107 repositories
- easystats (library) — 100 papers, 107 repositories
- UMAP (library) — 100 papers, 116 repositories
- ANTs (software) — 98 papers, 93 repositories
- car (library) — 97 papers, 109 repositories
- Optimization Toolbox (toolbox) — 96 papers, 102 repositories
- Keras (library) — 93 papers, 107 repositories
- rstatix (library) — 87 papers, 108 repositories
- psych (library) — 83 papers, 89 repositories
- limma (library) — 82 papers, 96 repositories
- tifffile (library) — 81 papers, 98 repositories
- Pingouin (library) — 79 papers, 97 repositories
- reticulate (library) — 76 papers, 87 repositories
- Tools for NIfTI and ANALYZE image (MATLAB) (toolbox) — 70 papers, 73 repositories
- edgeR (library) — 65 papers, 75 repositories
- SimpleITK (library) — 62 papers, 62 repositories
- SAMtools (software) — 61 papers, 75 repositories
- SingleCellExperiment (library) — 61 papers, 73 repositories
- GIfTI library for MATLAB (toolbox) — 59 papers, 49 repositories
- XGBoost (library) — 57 papers, 68 repositories
- AFNI (software) — 56 papers, 50 repositories
- Hugging Face Transformers (library) — 56 papers, 64 repositories
- Curve Fitting Toolbox (toolbox) — 54 papers, 58 repositories
- Harmony (library) — 53 papers, 60 repositories
- imageio (library) — 51 papers, 61 repositories
- caret (library) — 50 papers, 60 repositories
- BEDTools (software) — 47 papers, 54 repositories
- PyTorch Geometric (library) — 46 papers, 50 repositories
- SHAP (library) — 46 papers, 53 repositories
- shadedErrorBar (toolbox) — 44 papers, 52 repositories
- WGCNA (library) — 44 papers, 53 repositories
- Biopython (library) — 43 papers, 52 repositories
- CircStat (toolbox) — 42 papers, 46 repositories
- Psychtoolbox (toolbox) — 42 papers, 40 repositories
- Connectome Workbench (software) — 41 papers, 32 repositories
- PyTorch Lightning (library) — 41 papers, 47 repositories
- nlme (library) — 39 papers, 48 repositories
- fdr_bh (Benjamini-Hochberg FDR) (toolbox) — 38 papers, 34 repositories
- Violinplot-Matlab (toolbox) — 38 papers, 46 repositories
- ICLabel (toolbox) — 37 papers, 38 repositories
- survival (library) — 37 papers, 41 repositories
- Brain Connectivity Toolbox (toolbox) — 35 papers, 36 repositories
- glmnet (library) — 33 papers, 41 repositories
- mgcv (library) — 33 papers, 39 repositories
- Monocle 3 (library) — 33 papers, 36 repositories
- Nipype (library) — 33 papers, 31 repositories
- brms (library) — 32 papers, 40 repositories
- rpy2 (library) — 32 papers, 39 repositories
- pROC (library) — 31 papers, 37 repositories
- pydicom (library) — 31 papers, 33 repositories
- statannotations (library) — 31 papers, 33 repositories
- pysam (library) — 30 papers, 43 repositories
- xarray (library) — 30 papers, 33 repositories
- afex (library) — 28 papers, 33 repositories
- boundedline (toolbox) — 28 papers, 28 repositories
- BrainSpace (library) — 28 papers, 30 repositories
- lavaan (library) — 28 papers, 28 repositories
- PsychoPy (software) — 28 papers, 31 repositories
- Stan (software) — 28 papers, 35 repositories
- MRtrix3 (software) — 27 papers, 26 repositories
- STAR (software) — 27 papers, 27 repositories
- DIPY (library) — 26 papers, 30 repositories
- MONAI (library) — 26 papers, 30 repositories
- export_fig (toolbox) — 25 papers, 21 repositories
- neuromaps (library) — 25 papers, 24 repositories
- BayesFactor (library) — 24 papers, 27 repositories
- JAX (library) — 24 papers, 30 repositories
- randomForest (library) — 24 papers, 24 repositories
- cifti-matlab (toolbox) — 23 papers, 18 repositories
- BCFtools (software) — 22 papers, 27 repositories
- NEURON (software) — 22 papers, 28 repositories
- nnU-Net (software) — 22 papers, 19 repositories
- RDKit (library) — 22 papers, 22 repositories
- CuPy (library) — 21 papers, 24 repositories
- ggseg (library) — 21 papers, 23 repositories
- imbalanced-learn (library) — 20 papers, 25 repositories
- Neurodata Without Borders (PyNWB, MatNWB) (library) — 19 papers, 23 repositories
- PyBIDS (library) — 19 papers, 18 repositories
- PyWavelets (library) — 19 papers, 20 repositories
- Wavelet Toolbox (toolbox) — 19 papers, 20 repositories
- fMRIPrep (software) — 18 papers, 18 repositories
- LightGBM (library) — 18 papers, 21 repositories
- autoreject (library) — 17 papers, 19 repositories
- dcm2niix (software) — 17 papers, 18 repositories
- SpikeInterface (library) — 17 papers, 22 repositories
- Subread (featureCounts) (software) — 17 papers, 18 repositories
- tedana (library) — 17 papers, 6 repositories
- BrainSMASH (library) — 16 papers, 15 repositories
- Chronux (toolbox) — 16 papers, 18 repositories
- Distributions.jl (library) — 16 papers, 16 repositories
- MNE-BIDS (library) — 16 papers, 16 repositories
- neuroCombat (library) — 16 papers, 15 repositories
- Plots.jl (library) — 16 papers, 17 repositories
- scikit-posthocs (library) — 16 papers, 19 repositories
- specparam (formerly FOOOF) (library) — 16 papers, 22 repositories
- abagen (library) — 15 papers, 11 repositories
- metafor (library) — 15 papers, 18 repositories
- Neo (library) — 15 papers, 22 repositories
- scVelo (library) — 15 papers, 22 repositories
- Squidpy (library) — 15 papers, 21 repositories
- multcomp (library) — 14 papers, 19 repositories
- napari (software) — 14 papers, 15 repositories
- SymPy (library) — 14 papers, 17 repositories
- CAT12 (toolbox) — 13 papers, 10 repositories
- glmmTMB (library) — 13 papers, 15 repositories
- MNE-Connectivity (library) — 13 papers, 13 repositories
- Snakemake (software) — 13 papers, 15 repositories
- Deep Learning Toolbox (toolbox) — 12 papers, 12 repositories
- DifferentialEquations.jl (library) — 12 papers, 12 repositories
- PyRadiomics (library) — 12 papers, 12 repositories
- DataFrames.jl (library) — 11 papers, 11 repositories
- ERPLAB (toolbox) — 11 papers, 11 repositories
- FastQC (software) — 11 papers, 12 repositories
- netneurotools (library) — 11 papers, 11 repositories
- Nextflow (software) — 11 papers, 11 repositories
- PyMC (library) — 11 papers, 13 repositories
- AllenSDK (library) — 10 papers, 11 repositories
- ArviZ (library) — 10 papers, 13 repositories
- Brian 2 (library) — 10 papers, 12 repositories
- Cellpose (software) — 10 papers, 10 repositories
- CoSMoMVPA (toolbox) — 10 papers, 11 repositories
- GIFT (toolbox) — 10 papers, 8 repositories
- Makie (library) — 10 papers, 10 repositories
- Dcm2Bids (software) — 8 papers, 8 repositories
- ImageJ / Fiji (software) — 8 papers, 13 repositories
- Kilosort (software) — 8 papers, 9 repositories
- PyPREP (library) — 8 papers, 7 repositories
- Brainstorm (toolbox) — 7 papers, 8 repositories
- CaImAn (library) — 7 papers, 7 repositories
- DataLad (software) — 7 papers, 9 repositories
- deepTools (software) — 7 papers, 8 repositories
- NeuroDSP (library) — 7 papers, 8 repositories
- neuroHarmonize (library) — 7 papers, 6 repositories
- OHBA Software Library (OSL) (toolbox) — 7 papers, 10 repositories
- Pyro (library) — 7 papers, 8 repositories
- BIDS Validator (software) — 6 papers, 7 repositories
- Elephant (library) — 6 papers, 8 repositories
- MRIQC (software) — 6 papers, 5 repositories
- Open Ephys analysis tools (library) — 6 papers, 8 repositories
- pyRiemann (library) — 6 papers, 7 repositories
- RNifti (library) — 6 papers, 3 repositories
- Suite2p (software) — 6 papers, 7 repositories
- Flux.jl (library) — 5 papers, 5 repositories
- HCP Pipelines (software) — 5 papers, 4 repositories
- Phy (software) — 5 papers, 10 repositories
- pyABF (library) — 5 papers, 7 repositories
- pycortex (library) — 5 papers, 5 repositories
- BrainIAK (library) — 4 papers, 5 repositories
- Cell Ranger (software) — 4 papers, 6 repositories
- HeuDiConv (software) — 4 papers, 5 repositories
- JAGS (software) — 4 papers, 4 repositories
- LFPy (library) — 4 papers, 5 repositories
- MOABB (library) — 4 papers, 4 repositories
- NEST Simulator (software) — 4 papers, 6 repositories
- Nighres (library) — 4 papers, 4 repositories
- psignifit (library) — 4 papers, 6 repositories
- QSIPrep (software) — 4 papers, 5 repositories
- WFDB Python (library) — 4 papers, 5 repositories
- YASA (library) — 4 papers, 4 repositories
- Braindecode (library) — 3 papers, 4 repositories
- CONN (toolbox) — 3 papers, 3 repositories
- DPABI (toolbox) — 3 papers, 1 repository
- eegUtils (library) — 3 papers, 5 repositories
- GLMsingle (library) — 3 papers, 3 repositories
- LMFIT (library) — 3 papers, 4 repositories
- MDAnalysis (library) — 3 papers, 4 repositories
- MEEGkit (library) — 3 papers, 3 repositories
- NeuroKit2 (library) — 3 papers, 4 repositories
- Salmon (software) — 3 papers, 3 repositories
- TemplateFlow (library) — 3 papers, 3 repositories
- Bambi (library) — 2 papers, 3 repositories
- DeepLabCut (software) — 2 papers, 3 repositories
- MountainSort (software) — 2 papers, 2 repositories
- NetPyNE (library) — 2 papers, 2 repositories
- NiMARE (library) — 2 papers, 2 repositories
- nltools (library) — 2 papers, 2 repositories
- permuco (library) — 2 papers, 3 repositories
- The Virtual Brain (software) — 2 papers, 2 repositories
- Turing.jl (library) — 2 papers, 2 repositories
- jsPsych (library) — 1 paper, 1 repository
- Nengo (library) — 1 paper, 1 repository