jw156605
Computational biologist, Associate Professor at University of Michigan, and PI of @welch-lab. We develop novel computational methods for single cell genomics.
Pinned Repositories
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
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
scNMT
Validating Joint Analysis of Single-Cell Transcriptome and Epigenome Data Using scNMT-seq and SNARE-seq
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
liger
R package for integrating and analyzing multiple single-cell datasets
MultiVelo
Multi-omic velocity inference
PerturbNet
PerturbNet is a deep generative model that can predict the distribution of cell states induced by chemical or genetic perturbation
pyliger
Python package for integrating and analyzing multiple single-cell datasets (A Python version of LIGER)
VeloVAE
Deep Generative Modeling of RNA Velocity
jw156605's Repositories
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
jw156605/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
jw156605/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
jw156605/scNMT
Validating Joint Analysis of Single-Cell Transcriptome and Epigenome Data Using scNMT-seq and SNARE-seq
jw156605/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
jw156605/awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
jw156605/bioinf602-603-fall2020
Fall 2020 BIOINF List of Approved Papers
jw156605/bioinf602-603-wn2020
jw156605/BIRSBIO2020.scNMTseq.LIGER
BIRSBIO2020 workshop, scNMTseq data, LIGER analysis
jw156605/jw156605.github.io
jw156605/KEMA
code and data for the paper `Kernel Manifold Alignment for domain adaptation'
jw156605/nat
NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
jw156605/PerturbNet
PerturbNet is a deep generative model that can predict the distribution of cell states induced by chemical or genetic perturbation
jw156605/scoda
A streaming algorithm for community detection algorithm in very large networks
jw156605/SnapTools
A module for working with snap files in Python
jw156605/welchlab
Welch Lab
jw156605/whitePaper
Manubot for white paper