francois-a

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

feather

Feather: fast, interoperable binary data frame storage for Python, R, and more powered by Apache Arrow

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

anndata

Annotated data.

dynamo-release

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

SpliceAI

A deep learning-based tool to identify splice variants

pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization

phaser

phasing and Allele Specific Expression from RNA-seq

pandas-plink

PLINK reader for Python.

SignatureAnalyzer

Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.

LCV

Software implementing the Latent Causal Variable Model

qtltools

A complete tool set for molecular QTL discovery and analysis

rpvg

Method for inferring path posterior probabilities and abundances from pangenome graph read alignments

gtex-v8

Notebooks and scripts for reproducing analyses and figures from the V8 GTEx Consortium paper

pyqtl

Collection of analysis tools for quantitative trait loci

RNA_MUTECT_1.0-1

xqtl-pipeline

Molecular QTL data analysis pipeline developed for ADSP functional genomic xQTL consortium

MendelianRNA-seq

table-testing

requirements, examples, and tests for expression matrix file formats

gtex-single-nucleus-reference

Code repository for the snRNA-seq cross-tissue atlas project

dalmatian

dalmatian is a collection of high-level companion functions for Firecloud and FISS.

SpliceAI-lookup

Website for checking SpliceAI and Pangolin scores:

canine

A modular, high-performance computing solution to run jobs using SLURM

rnaseq-utils

Utilities for RNA-seq analyses

SMM_clustering_2020

Repo for analysis of SMM DNA + RNA data.