Repositories list

• rhopca

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •0•7•0•0•Updated Mar 31, 2026Mar 31, 2026

• gget

  Public
  🧬 gget enables efficient querying of genomic reference databases

  rna-seqgenomicsreference+ 13

  rna-seqgenomicsreferencedatabasesensemblproteomicsblasttranscriptomicsuniprotncbi+ 6

  Python

  •

  BSD 2-Clause "Simplified" License

  •85•1.1k•22•1•Updated Mar 31, 2026Mar 31, 2026

• BI-BE-CS-183-2026

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

  Jupyter Notebook

  •

  Other

  •77•2•0•0•Updated Mar 31, 2026Mar 31, 2026

• wompwomp

  Public
  R

  •

  Other

  •1•28•0•0•Updated Mar 30, 2026Mar 30, 2026

• monod

  Public
  The Monod package fits CME models to sequencing data.

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •7•33•3•0•Updated Mar 30, 2026Mar 30, 2026

• biowomp

  Public
  R

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated Mar 30, 2026Mar 30, 2026

• radiology_dataset_db

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated Mar 29, 2026Mar 29, 2026

• tcia-radiology-processing

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated Mar 26, 2026Mar 26, 2026

• seqspec

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

  Python

  •

  MIT License

  •18•128•0•1•Updated Mar 26, 2026Mar 26, 2026

• CJP_2025

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Mar 24, 2026Mar 24, 2026

• OP_2025_2

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Mar 20, 2026Mar 20, 2026

• cellsweep

  Public
  Jupyter Notebook

  •0•20•0•0•Updated Mar 19, 2026Mar 19, 2026

• voyager

  Public
  From geospatial to spatial -omics

  rexploratory-data-analysisspatial+ 9

  rexploratory-data-analysisspatialedarstatsbioconductorr-packageomicstranscriptomicsspatial-statistics+ 2

  R

  •

  Artistic License 2.0

  •14•101•22•0•Updated Mar 18, 2026Mar 18, 2026

• LSCHWCP_202391

  Public
  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Mar 18, 2026Mar 18, 2026

• kallisto

  Public
  Near-optimal RNA-Seq quantification

  rna-seqkallistopseudoalignment

  rna-seqkallistopseudoalignment

  C

  •

  BSD 2-Clause "Simplified" License

  •181•755•200•13•Updated Mar 16, 2026Mar 16, 2026

• kb_docs

  Public
  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated Mar 12, 2026Mar 12, 2026

• LSCHWCP_2023

  Public
  Identification of viral RdRPs in single-cell RNA sequencing data

  viruskallistotranslated+ 4

  viruskallistotranslatedviralpalmdbtranslated-alignmentcomma-free-code

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •2•13•1•0•Updated Mar 12, 2026Mar 12, 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

  •28•186•3•0•Updated Mar 11, 2026Mar 11, 2026

• kallistobustools

  Public
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data

  rna-seqsingle-cellkallisto+ 1

  rna-seqsingle-cellkallistobustools

  MIT License

  •28•120•29•1•Updated Mar 10, 2026Mar 10, 2026

• SpatialFeatureExperiment

  Public
  Extension of SpatialExperiment with sf

  R

  •

  Artistic License 2.0

  •14•57•27•0•Updated Mar 7, 2026Mar 7, 2026

• XgenePy

  Public
  Jupyter Notebook

  •0•2•0•0•Updated Mar 5, 2026Mar 5, 2026

• XgeneR

  Public
  HTML

  •

  BSD 2-Clause "Simplified" License

  •0•3•0•0•Updated Mar 5, 2026Mar 5, 2026

• edgePython

  Public
  edgePython is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data. It also includes a new single-cell dif…

  Python

  •

  GNU General Public License v3.0

  •3•52•0•1•Updated Mar 2, 2026Mar 2, 2026

• FCSKPP_2025

  Public
  R

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

• gget_examples

  Public
  Examples for gget (https://github.com/pachterlab/gget).

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •6•39•0•0•Updated Feb 20, 2026Feb 20, 2026

• 8cubeDB

  Public
  Query gene specificity in the founder mouse strains

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•2•0•0•Updated Feb 12, 2026Feb 12, 2026

• GP_2023

  Public
  Switching processes

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

• HCP_2024

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•2•0•0•Updated Jan 28, 2026Jan 28, 2026

• OBP_2025

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated Jan 26, 2026Jan 26, 2026

• LP_2021

  Public
  TeX

  •

  BSD 2-Clause "Simplified" License

  •6•53•1•0•Updated Jan 15, 2026Jan 15, 2026