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nsd2_req_subunit

Code for Paper : NSD2 is a requisite subunit of the AR/FOXA1 neo-enhanceosome in promoting prostate tumorigenesis

https://github.com/mctp/nsd2_req_subunit

Science Score: 52.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization mctp has institutional domain (pathology.med.umich.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Code for Paper : NSD2 is a requisite subunit of the AR/FOXA1 neo-enhanceosome in promoting prostate tumorigenesis

Basic Info
  • Host: GitHub
  • Owner: mctp
  • License: apache-2.0
  • Language: R
  • Default Branch: main
  • Size: 35.2 KB
Statistics
  • Stars: 2
  • Watchers: 4
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

NSD2reqsubunit

Code Repository for Paper : NSD2 is a requisite subunit of the AR/FOXA1 neo-enhanceosome in promoting prostate tumorigenesis

Paper Citation goes here.

Repo Contents

RNA-Seq

RunRNAseqkallisto.sh - basic pseudo alignment

bulkRNA_Rscripts.R - R >3.6.0, additional analysis on bulk RNA data, GSEA, volcano outputs

ChIP-Seq

ChipAlignment_PE.sh - Basic alignment paired end pipeline (bwamem, samtools, picard wrapper)

EnrichmentHeatmaps.sh - Uses Deeptools to create heatmaps

OverlapCompare.R - Uses R>3.6.0 to implement a combination of ChipPeakAnno and ChipSeeker packages to compare output from MACS peak calling

Run_HOMER.sh - Runs HOMER motif analysis

TrackPlot.R - Uses R> 4.0.1 and R package Sushi to generate IGV style tracks with labeled motifs.

Copy of version information for software/tools needed to run these. Cites.

Owner

  • Name: MCTP
  • Login: mctp
  • Kind: organization
  • Email: mctp-github@umich.edu
  • Location: Pathology Department University of Michigan

Michigan Center for Translational Pathology (MCTP)

Citation (CITATION.cff) 

cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "MCTP"
title: "NSD2_req_subunit"
version: 1.0.0
doi: 10.5281/zenodo.1234
date-released: 2024-07-26
url: "https://github.com/mctp/NSD2_req_subunit"

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