Pinned Repositories
signac
R toolkit for the analysis of single-cell chromatin data
Arabidopsis-TE-variants
Analysis of TE presence/absence data
biorxivData
A look at some bioRxiv metrics
methylQC
Quality control for methylome data
ngs-tools
Miscellaneous tools for genomics
notebook-template
Template for a computational lab notebook using bookdown
signac-paper
Code to reproduce analyses shown in the Signac paper
sinto
Tools for single-cell data processing
SNARE-seq
Code to process raw SNARE-seq ATAC reads
UCLA-T32
UCLA T32 Single-Cell Analysis Workshop
timoast's Repositories
timoast/sinto
Tools for single-cell data processing
timoast/notebook-template
Template for a computational lab notebook using bookdown
timoast/SNARE-seq
Code to process raw SNARE-seq ATAC reads
timoast/ngs-tools
Miscellaneous tools for genomics
timoast/signac-paper
Code to reproduce analyses shown in the Signac paper
timoast/UCLA-T32
UCLA T32 Single-Cell Analysis Workshop
timoast/Arabidopsis-TE-variants
Analysis of TE presence/absence data
timoast/biorxivData
A look at some bioRxiv metrics
timoast/methylQC
Quality control for methylome data
timoast/sctools
Single cell RNA-seq tools
timoast/TE-cistrome
Analysis of transcription factor bindng sites within transposable elements
timoast/TEpy
Uses paired-end sequencing data to find transposable element variants
timoast/epi-immune
Processing pipeline for public multiome and scATAC-seq immune datasets
timoast/frag-spec
Fragment file format specification
timoast/timoast.github.io
My site
timoast/atac-cnn
Analysis of cell-type-specific DNA accessibility peaks with convolutional neural nets
timoast/basc
Processing pipeline for single-cell barcoded Tn5 assays
timoast/BICCN
Code to process raw scATAC-seq data from BICCN
timoast/methylQC-shiny
Web app for the methylQC package
timoast/MPAL-hg38
Re-mapping of Granja et al. (2019) scATAC-seq data to hg38
timoast/multi-ct
Re-processing single-cell multiCUT&Tag data from Gopalan et al. 2021
timoast/NGS-Library-Quantitation
IPython notebook for NGS library quantitation by qPCR
timoast/npq-qtl
Analysis of structural rearrangements in NPQ promoter
timoast/salt-stress
Analysis of ATAC data for Arabidopsis salt stress
timoast/scg_lib_structs
Collections of library structure and sequence of popular single cell genomic methods
timoast/seurat-object
timoast/stuart
Personal R package