Pachter Lab

pachterlab

Pasadena, CA

http://pachterlab.github.io

Pachter Lab's repositories

gget

🧬 gget enables efficient querying of genomic reference databases

Language:PythonBSD-2-Clause852 11 57

ffq

A tool to find sequencing data and metadata from public databases.

Language:PythonMIT524 13 46

kb_python

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

Language:PythonBSD-2-Clause140 12 166

seqspec

machine-readable file format for genomic library sequence and structure

Language:PythonMIT92 8 16

voyager

From geospatial to spatial -omics

Language:RArtistic-2.060 4 30

LP_2021

Language:TeXBSD-2-Clause43 5 7

SpatialFeatureExperiment

Extension of SpatialExperiment with sf

Language:RArtistic-2.027 5 35

gget_examples

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

Language:Jupyter NotebookBSD-2-Clause25 4 2

monod

The Monod package fits CME models to sequencing data.

Language:PythonBSD-2-Clause2200

splitcode

Flexible and efficient parsing, interpreting and editing of sequencing reads

Language:CBSD-2-Clause18 2 7

RMEJLBASBMP_2024

Repository for the paper "The impact of package selection and versioning on single-cell RNA-seq analysis"

Language:Jupyter NotebookBSD-2-Clause1200

CGCCP_2023

scVI extension for unspliced RNA

Language:Jupyter NotebookBSD-2-Clause10 40

monod_examples

Tutorials for the Monod package, which fits CME models to sequencing data.

Language:Jupyter NotebookBSD-2-Clause6 2 2

museumst

Museum of Spatial Transcriptomics

Language:RBSD-2-Clause6 4 3

GCCP_2022

Language:RoffBSD-2-Clause5 40

biophysics

Language:PythonBSD-2-Clause4 40

GBP_2024

Language:Jupyter NotebookBSD-2-Clause4 20

BGP_2024

Language:Jupyter NotebookBSD-2-Clause3 20

LP_2024

Language:Jupyter NotebookBSD-2-Clause3 10

CWGFLHGCCHAP_2021

Language:Jupyter NotebookBSD-2-Clause2 50

SFEData

Example SpatialFeatureExperiment datasets

Language:RArtistic-2.02 4 1

.github

1 20

BI-1C-2024

Language:Jupyter NotebookBSD-2-Clause100

FGP_2023

Language:Jupyter NotebookBSD-2-Clause1 20

FGP_2024

Language:Jupyter Notebook1 20

HSSHMP_2024

Code for reproducing the results in the second version of the preprint "Accurate quantification of single-nucleus and single-cell RNA-seq transcripts"

Language:Jupyter NotebookBSD-2-Clause1 30

LSCHWCP_2023

Identification of viral RNA in single-cell RNA sequencing data

Language:Jupyter NotebookBSD-2-Clause1 20

CGP_2023

Repository for meK-Means Inference Method

Language:Jupyter NotebookBSD-2-Clause020

LHKP_2023

Language:Jupyter NotebookBSD-2-Clause010

splitcode-tutorial

Language:Jupyter Notebook020