Repositories list

• clrcycle

  Public

  pachterlab/clrcycle’s past year of commit activity
  Python

  •11 fork•33 stars•00 issues•11 pull request•Updated Aug 28, 2026Aug 28, 2026

• paperpush

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •77 forks•160160 stars•00 issues•00 pull requests•Updated Aug 27, 2026Aug 27, 2026

• wompwomp

  Public
  R

  •

  Other

  •11 fork•3131 stars•00 issues•00 pull requests•Updated Aug 25, 2026Aug 25, 2026

• varseek

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •11 fork•2020 stars•00 issues•00 pull requests•Updated Aug 24, 2026Aug 24, 2026

• span

  Public
  Python

  •

  Apache License 2.0

  •22 forks•1818 stars•00 issues•00 pull requests•Updated Aug 21, 2026Aug 21, 2026

• edgePython

  Public
  Repository for edgePython which is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data.

  Python

  •

  GNU General Public License v3.0

  •77 forks•9191 stars•00 issues•00 pull requests•Updated Aug 21, 2026Aug 21, 2026

• ROP_2025

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 18, 2026Aug 18, 2026

• radiology_dataset_db

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 14, 2026Aug 14, 2026

• wompywompy

  Public
  Jupyter Notebook

  •00 forks•33 stars•00 issues•00 pull requests•Updated Aug 14, 2026Aug 14, 2026

• tcia-radiology-processing

  Public

  pachterlab/tcia-radiology-processing’s past year of commit activity
  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 13, 2026Aug 13, 2026

• ctkit

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 13, 2026Aug 13, 2026

• varseek-examples

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 13, 2026Aug 13, 2026

• cellsweep

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •00 forks•2626 stars•00 issues•00 pull requests•Updated Aug 8, 2026Aug 8, 2026

• P_2026_Bandelt-Dress

  Public
  Lean

  •

  BSD 2-Clause "Simplified" License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Aug 3, 2026Aug 3, 2026

• voyager

  Public
  From geospatial to spatial -omics

  rexploratory-data-analysisspatial+ 9

  rexploratory-data-analysisspatialedarstatsbioconductorr-packageomicstranscriptomicsspatial-statistics+ 2

  R

  •

  Artistic License 2.0

  •1616 forks•103103 stars•2323 issues•11 pull request•Updated Jul 24, 2026Jul 24, 2026

• ember

  Public
  ember: Entropy Metrics for Biological ExploRation

  Python

  •

  BSD 2-Clause "Simplified" License

  •11 fork•88 stars•00 issues•00 pull requests•Updated Jul 21, 2026Jul 21, 2026

• SBRGKLAYWMP_2025

  Public
  Code to generate figures for Swarna et al. 2025

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 21, 2026Jul 21, 2026

• seqspec

  Public
  machine-readable file format for genomic library sequence and structure

  Python

  •

  MIT License

  •2020 forks•130130 stars•11 issue•22 pull requests•Updated Jul 15, 2026Jul 15, 2026

• kallisto

  Public
  Near-optimal RNA-Seq quantification

  rna-seqkallistopseudoalignment

  rna-seqkallistopseudoalignment

  C

  •

  BSD 2-Clause "Simplified" License

  •183183 forks•769769 stars•200200 issues•1313 pull requests•Updated Jul 12, 2026Jul 12, 2026

• BHGP_2022

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •11 fork•1010 stars•00 issues•00 pull requests•Updated Jun 24, 2026Jun 24, 2026

• fastQpick

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •00 forks•3232 stars•00 issues•00 pull requests•Updated Jun 21, 2026Jun 21, 2026

• kb_python

  Public
  A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

  scrna-seqkallistosingle-cell-rna-seq+ 3

  scrna-seqkallistosingle-cell-rna-seqrna-velocity-estimationbustoolskb-python

  Python

  •

  BSD 2-Clause "Simplified" License

  •3030 forks•192192 stars•00 issues•00 pull requests•Updated Jun 9, 2026Jun 9, 2026

• pachterlab.github.io

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 9, 2026Jun 9, 2026

• HCP_2024

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jun 9, 2026Jun 9, 2026

• P_2026_2

  Public
  Optimal pebbling number of the hypercube

  Lean

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 6, 2026Jun 6, 2026

• XgenePy

  Public
  Jupyter Notebook

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jun 3, 2026Jun 3, 2026

• XgeneR

  Public
  HTML

  •

  BSD 2-Clause "Simplified" License

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jun 3, 2026Jun 3, 2026

• BI-BE-CS-183-2026

  Public
  Introduction to Computational Biology and Bioinformatics Course at Caltech, 2026

  Jupyter Notebook

  •

  Other

  •7979 forks•55 stars•00 issues•00 pull requests•Updated Jun 3, 2026Jun 3, 2026

• BHGP_2022_v1

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •22 forks•2323 stars•22 issues•00 pull requests•Updated May 21, 2026May 21, 2026

• klue

  Public
  HTML

  •

  BSD 2-Clause "Simplified" License

  •00 forks•55 stars•00 issues•00 pull requests•Updated May 13, 2026May 13, 2026