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append

AppEnD tool for mapping 3’ additions from RNA-seq data. See details in Welch et al., RNA 2015: http://rnajournal.cshlp.org/content/21/7/1375.abstract

awesome-single-cell

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

bioinf602-603-fall2020

Fall 2020 BIOINF List of Approved Papers

bioinf602-603-wn2020

birsbio2020.scnmtseq.liger

BIRSBIO2020 workshop, scNMTseq data, LIGER analysis

jw156605.github.io

kema

code and data for the paper `Kernel Manifold Alignment for domain adaptation'

matcher

MATCHER (Manifold Alignment to Characterize Experimental Relationships) is an approach for integrating single cell transcriptomic and epigenomic data. See Welch et al. (2017) for more details: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1269-0

nat

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

perturbnet

PerturbNet is a deep generative model that can predict the distribution of cell states induced by chemical or genetic perturbation

scnmt

Validating Joint Analysis of Single-Cell Transcriptome and Epigenome Data Using scNMT-seq and SNARE-seq

scoda

A streaming algorithm for community detection algorithm in very large networks

singlesplice

Algorithm for detecting alternative splicing in a population of single cells. See details in Welch et al., Nucleic Acids Research 2016: http://nar.oxfordjournals.org/content/early/2016/01/05/nar.gkv1525.full

slicer

SLICER algorithm for inferring cell trajectories. See details in Welch et al., Genome Biology 2016: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0975-3

snaptools

A module for working with snap files in Python

welchlab

Welch Lab

whitepaper

Manubot for white paper