timoast

sinto

Tools for single-cell data processing

notebook-template

Template for a computational lab notebook using bookdown

SNARE-seq

Code to process raw SNARE-seq ATAC reads

ngs-tools

Miscellaneous tools for genomics

signac-paper

Code to reproduce analyses shown in the Signac paper

UCLA-T32

UCLA T32 Single-Cell Analysis Workshop

Arabidopsis-TE-variants

Analysis of TE presence/absence data

biorxivData

A look at some bioRxiv metrics

methylQC

Quality control for methylome data

sctools

Single cell RNA-seq tools

TE-cistrome

Analysis of transcription factor bindng sites within transposable elements

TEpy

Uses paired-end sequencing data to find transposable element variants

epi-immune

Processing pipeline for public multiome and scATAC-seq immune datasets

frag-spec

Fragment file format specification

timoast.github.io

My site

atac-cnn

Analysis of cell-type-specific DNA accessibility peaks with convolutional neural nets

basc

Processing pipeline for single-cell barcoded Tn5 assays

BICCN

Code to process raw scATAC-seq data from BICCN

methylQC-shiny

Web app for the methylQC package

MPAL-hg38

Re-mapping of Granja et al. (2019) scATAC-seq data to hg38

multi-ct

Re-processing single-cell multiCUT&Tag data from Gopalan et al. 2021

NGS-Library-Quantitation

IPython notebook for NGS library quantitation by qPCR

npq-qtl

Analysis of structural rearrangements in NPQ promoter

salt-stress

Analysis of ATAC data for Arabidopsis salt stress

scg_lib_structs

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

seurat-object

stuart

Personal R package