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aschrom

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

awesome_spatial_omics

tools and notes for spatial omics

brie

BRIE: Bayesian Regression for Isoform Estimate in Single Cells

cell_type_enrichment_pipeline

configs

Config files used to define parameters specific to compute environments at different Institutions

crc

destiny

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/destiny.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=destiny.

encodegsc

Genome Structure Correction

floriddia_et_al_2019

hello_world

a repository

hla-la

Fast HLA type inference from whole-genome data

hmmratac

HMMRATAC peak caller for ATAC-seq data

input-wacom

Linux kernel driver for Wacom devices

intropolis

Exon-exon splice junctions across SRA

jaekel_agirre_et_al_2018

Code and data from the manuscript (Jäkel and Agirre et. al. 2019, Altered human oligodendrocyte heterogeneity in multiple sclerosis.)

ldsc

LD Score Regression (LDSC)

ldsc_corces_etal_adpd

Code for LD score regression analyses performed in analyses presented in manuscript

meijer_agirre_scataceae_2020

Code and data from Meijer and Agirre et al.

mpra_oligo_barcode_pipeline

mpraflow

A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data

mpranalyze

Analyse enhancer strength based on MPRA experiments.

popscle

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

samap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.

sc3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

scasl

single-cell clustering based on alternative splicing landscapes

scim

Code for Universal Single-Cell Matching with Unpaired Feature Sets

shinycell

Shiny Interactive Web Apps for Single-Cell Data

shinymultiomeuio

ShinyMultiomeUiO Shiny R based web tool for

smartseq2

A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.