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concordexr

R implementation of the concordex python command line tool

covid19-county

COVID-19 data from LA County

cp_2021

Code for reproducing the results in "The Split Senate" paper

cp_2023

cwgflhgcchap_2021

dballsmrdmcmgwstpmbdkpfp_2023

express

Streaming fragment assignment for real-time analysis of sequencing experiments

ffq

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

gccp_2022

gfcp_2022

RNA velocity validation

gget

🧬 gget enables efficient querying of genomic reference databases

gget_examples

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

gp_2020

Code to reproduce results in the paper "Special Function Methods for Bursty Models of Transcription"

gp_2020_2

Intrinsic/extrinsic noise mini-project

gp_2021

Gamma-OU Gillespie mini-project.

gp_2021_2

CME solution for splicing DAGs coupled to a bursting gene.

gp_2021_3

gp_2021_4

gp_2023

Switching processes

gpctp_2019

Notebooks for reproducing figures and results from the paper Gehring et al., Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins, Nature Biotechnology (2019) doi:10.1038/s41587-019-0372-z

gpctp_2019-2

grnp_2020

Repository for reproducing the results and figures in Gustafsson et al. 2020

gsp_2019

Code for reproducing results from the paper "RNA velocity and protein acceleration from single-cell multiomics experiments."

gvfp_2021

SDE comparison preprint

gvp_2023

scRNA-seq, regulation, and sysbio

gyp_2022

hpm_2022

Simulations of the robustness of AAQuant to noise

hshmp_2022

htsdiagnostics

Software for diagnostic testing based on high-throughput sequencing

isolate_transcripts