Pachter Lab

gget

🧬 gget enables efficient querying of genomic reference databases

kallisto

Near-optimal RNA-Seq quantification

ffq

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

kb_python

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

seqspec

machine-readable file format for genomic library sequence and structure

voyager

From geospatial to spatial -omics

picasso

Picasso: a methods for embedding points in 2D in a way that respects distances while fitting a user-specified shape.

splitcode

Flexible and efficient parsing, interpreting and editing of sequencing reads

SpatialFeatureExperiment

Extension of SpatialExperiment with sf

monod

The Monod package fits CME models to sequencing data.

qcbc

concordex

Identification of spatial homogeneous regions

CGCCP_2023

scVI extension for unspliced RNA

concordexR

Compute the neighborhood consolidation matrix and identify SHRs

biophysics

Repository for Pachter Lab Biophysics

monod_examples

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

JBMMCKP_2023

LP_2024

LSRRSRLFKOTWMWMP_2024

Repository for reproducing results for lr-kallisto

SHSOHMP_2024

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

FGP_2024

CGP_2023

Repository for meK-Means Inference Method

.github

FGP_2023

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"

kb_docs

LSCHWCP_2023

Identification of viral RNA in single-cell RNA sequencing data

Chronocell

pachterlab.github.io

splitcode-tutorial