jw156605

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

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

scNMT

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

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'

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

scoda

A streaming algorithm for community detection algorithm in very large networks

SnapTools

A module for working with snap files in Python

welchlab

Welch Lab

whitePaper

Manubot for white paper