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qbrc-somatic-pipeline

QBRC Somatic Mutation Calling Pipeline

raincloudplots

Code and tutorials to visualise your data that is both beautiful *and* statistically valid

recount3

Explore and download data from the recount3 project

repac

rna-bloom

:hibiscus: reference-free transcriptome assembly for short and long reads

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

sasquatch

Predicting the impact of regulatory SNPs from cell and tissue specific DNase-footprints

sc-gc

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scapture

scarches

Reference mapping for single-cell genomics

scatac-pro

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

scatac-seq

sccancer

A package for automated processing of single cell RNA-seq data in cancer

sccrc_continuum

scdapars

Dynamic Analysis of Alternative Polyadenylation from single-cell RNA-seq (scDaPars)

scell_lung_adenocarcinoma

This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset

scg_lib_structs

Collections of library structure and sequence of popular single cell genomic methods

scidata_scrnaseq

scissor

Scissor package

sclapa

scmapa

scmetabolism

Quantifying metabolism activity at the single-cell resolution

scmgca

"Topological Identification and Interpretation for Single-cell Gene Regulation Elucidation across Multiple Platforms using scMGCA" in Nature Communications 2023

scminer

Single-cell Mutual Information-based Network Engineering Ranger

scp

Single Cell Pipeline

scpage

scplc

Codes for the scPLC project

scrna-seq_notes

A list of scRNA-seq analysis tools

scrna-tools

Table of software for the analysis of single-cell RNA-seq data.