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awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

computational-statistics

Methods for computational statistics. Optimization, EM, MCMC, Bayesian Modeling, Variational inference.

datasharing

The Leek group guide to data sharing

gvcf_pipeline-nf

Nextflow pipeline for generate GVCF from BAM with GenomeAnalysisTK with step of realignment

hernet.github.io

jz-native-mobile-apps

Native JavaZone apps for Android and iOS

pyscenic

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

saucie

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

scvi

Deep generative modeling for single-cell transcriptomics

seqc

Single-Cell Sequencing Quality Control and Processing Software

singleflow

SingleFlow is a pipeline for analyzing scRNA-seq data.

transcriptional-map-nk

We describe a transcriptional reference map of human natural killer (NK) cells based on analysis of scRNA-seq data from both blood and tissue. We also analyze data from various solid tumors and map these onto this reference.

trvae

Conditional Out-of-Sample prediction

txpp

Pipeline for preprocessing of scRNA-seq 10x genomics FASTQ files. Produces loom files with counts of spliced and unspliced transcripts (for RNA velocity computation) as well as an expression count matrix.