Pinned Repositories
Analysis-Flow
NextFlow pipeline for automated analysis of processed RNA-Seq and Nascent data
ChIP-Flow
Nextflow pipeline for ChIP-seq analysis.
codeclub
Collected Resources for Dowell Lab Code Clubs
DAStk
Differential ATAC-seq toolkit
FStitch
Fast Stitch Reader (FStitch) -- fast-processing tool written in C for the annotation of regions of active transcription.
mumerge
muMerge tool for combining replicate bed-regions
Nascent-Flow
Nascent Transcription Processing Pipeline
RNAseq-Flow
Nextflow pipeline for processing RNA-seq data
srworkshop
Scripts and files for the annual Short Read Analysis Workshop
TFEA
Transcription Factor Enrichment Analysis
Dowell Lab's Repositories
Dowell-Lab/TFEA
Transcription Factor Enrichment Analysis
Dowell-Lab/DAStk
Differential ATAC-seq toolkit
Dowell-Lab/srworkshop
Scripts and files for the annual Short Read Analysis Workshop
Dowell-Lab/Nascent-Flow
Nascent Transcription Processing Pipeline
Dowell-Lab/RNAseq-Flow
Nextflow pipeline for processing RNA-seq data
Dowell-Lab/ChIP-Flow
Nextflow pipeline for ChIP-seq analysis.
Dowell-Lab/mumerge
muMerge tool for combining replicate bed-regions
Dowell-Lab/Allen_Peptide_2022
Dowell-Lab/Analysis-Flow
NextFlow pipeline for automated analysis of processed RNA-Seq and Nascent data
Dowell-Lab/codeclub
Collected Resources for Dowell Lab Code Clubs
Dowell-Lab/Fant_2019_Analysis
Supplemental code used for analysis in Fant 2019 (unpublished)
Dowell-Lab/Bidirectional-Flow
Nextflow pipeline for detecting bidirectional transcripts from nascent RNA sequencing data.
Dowell-Lab/Bidir_Counting_Analysis
This repo includes the generalizable pipeline for identification, counting, and length assessments of Bidirectionals from nascent RNA seq data
Dowell-Lab/bidir_gene_pairs
Bidirectional transcript and gene pairs derived from nascent RNA data
Dowell-Lab/bidirectionals_merged
Generates a final merged file from bidirectionals called by Tfit and dREG across multiple samples after paper muMerge.
Dowell-Lab/CDK7_inhibition
Scripts and code used to analyze data in CDK7 inhibition project
Dowell-Lab/DBNascent-build
Python scripts and utilities for building DBNascent in MySQL
Dowell-Lab/DBNascent_Analysis
Contains meta analyses performed using data in DBNascent
Dowell-Lab/DeconvolutionNascent
Deconvolution of Nascent Sequencing Data Using Transcriptional Regulatory Elements
Dowell-Lab/Downfile_pipeline
Nextflow pipeline for making bedgraphs and tdfs from CRAMs/BAMs
Dowell-Lab/DS_Normalization
Scripts relating to differential expression in trisomy 21 cells
Dowell-Lab/motif_scanning_and_distances
The code used to generate the motif information used in the DBNascent repository paper for TRN TF anchoring.
Dowell-Lab/Protocol-Comparisons
This repository contains code used for the comparisons of nascent RNA capture protocols.
Dowell-Lab/psea
Participant set enrichment analysis
Dowell-Lab/snpconnecter
Method for linking GWAS SNPs to genes based on DBNascent bidirectional region and gene pairs.
Dowell-Lab/sr2019jupyter
short read 2019 jupyter notebook
Dowell-Lab/sr2021
These are the scripts we used in the short read 2021 class
Dowell-Lab/TF_profiler
Dowell-Lab/Tfit
A tool for modeling and annotating RNA polymerase II behavior
Dowell-Lab/virtual_spike_in
Code for the "virtual spike in" normalization method using the ends of long genes