https://github.com/databio/awesome-nascent-rna-analysis
A collection of tools, pipelines, and guides for performing nascent RNA sequencing analysis
https://github.com/databio/awesome-nascent-rna-analysis
List: awesome-nascent-rna-analysis
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A collection of tools, pipelines, and guides for performing nascent RNA sequencing analysis
- Host: GitHub
- URL: https://github.com/databio/awesome-nascent-rna-analysis
- Owner: databio
- Created: 2022-04-18T16:31:47.000Z (about 4 years ago)
- Default Branch: master
- Last Pushed: 2022-04-18T16:52:31.000Z (about 4 years ago)
- Last Synced: 2025-10-21T23:01:56.308Z (8 months ago)
- Size: 1.95 KB
- Stars: 6
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Awesome Nascent RNA-seq analysis
A collection of tools, pipelines, and guides for performing nascent RNA sequencing analysis
# Raw data processing pipelines
- [Nascent-Flow](https://github.com/Dowell-Lab/Nascent-Flow): Nextflow Implementation of the Dowell Lab Nascent Pipeline.
- [nf-core Nascent](https://github.com/nf-core/nascent): nascent transcription processing pipeline built using Nextflow.
- [NRSA](http://bioinfo.vanderbilt.edu/NRSA/): analyze nascent transcription profiles generated by PRO-seq and GRO-seq data. NRSA quantifies nascent transcription for known genes, and detects, annotates, and quantifies active enhancers. NRSA predicts enhancer targets based on the closest TSS and/or using enhancer-TSS associations from FANTOM5 and 4DGenome where available.
- [PEPPRO](http://peppro.databio.org/en/latest/): a pipeline for PRO-seq, GRO-seq, and ChRO-seq data that is optimized on unique features of nascent RNA to be fast and accurate. It performs variable-length UMI adapter removal, read deduplication, trimming, mapping, QC, and signal tracks (bigWig) for plus and minus strands using mappability-scaled or unscaled read counts.
- [Proseq2.0](https://github.com/Danko-Lab/proseq2.0): Preprocesses and aligns run-on sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing.
# Read quantification
- [DENR](https://github.com/CshlSiepelLab/DENR): performs annotation based transcript level quantification on nascent RNA sequencing data. Explains observed polymerase density as a weighted mixture of the underlying transcript annotations.
# Region based annotations
- [FStitch](https://github.com/Dowell-Lab/FStitch): Fast Stitch Reader (FStitch) rapidly processes read coverage files into contigs of active and inactive regions of transcription. Intended for refining annotations in nascent transcription data.
- [Tfit](https://github.com/Dowell-Lab/Tfit): Annotate sites of bidirectional transcription
# Identifying regulatory elements
- [dReg](https://github.com/Danko-Lab/dREG): Detection of Regulatory DNA Sequences using GRO-seq Data.
# Differential analyses
- [tfTarget](https://github.com/Danko-Lab/tfTarget): identify differentially regulated TF networks based on comparative conditions (e.g. Treatment -vs- Control).
# Simulating nascent sequencing
- [nascentRNASim](https://github.com/CshlSiepelLab/nascentRNASim): simulate nascent RNA-seq based on empirical data.
# Guides and walkthroughs
- [GRO-seq guide](http://homer.ucsd.edu/homer/ngs/groseq/groseq.html): GRO-seq analysis guide with HOMER.