nc_timecourse
Updated git with cleaned NC_Timecourse Repo
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.2%) to scientific vocabulary
Repository
Updated git with cleaned NC_Timecourse Repo
Basic Info
- Host: GitHub
- Owner: Austin-s-h
- Language: R
- Default Branch: main
- Size: 52.2 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
Publication Release: 
Neural Crest Timecourse Analysis
This repository is broken down into 3 sections - RNA-Seq Data Processing and Analysis (./RNA-Seq) - CUT&RUN Data Processing and Analysis (./CUT-RUN) - ATAC-Seq Data Processing and Analysis (./ATAC-Seq)
In each of these folders, you will find invidual Rmd notebooks for various analyses including... - Differential Expression / Binding - Transcription Factor motif enrichment using HOMER and ChromVAR - hint-ATAC footprinting - Calculation of fragment length distribution - Calculation of putative Peak to Gene Enhancer-Promoter linkages (RNA-Seq and ATAC-Seq integration) - Genomic Overlapping and Clustering
The processing scripts for each genomic sample type are found as individual bash scripts within their respective folders. These contain... - File Parsing - Adapter/Quality Trimming - Alignment - Duplication Marking and Removal - Calculation of BigWigs - Calling Peaks - Quality Control
If you reference any of these scripts or utilze methods developed from this codebase, please cite: DEVCELLPUBLICATION_REFERENCE or
Hovland, A., & Bhattacharya, D. (2022). NC_Timecourse (Version 1.0.0) [Computer software]. https://doi.org/10.5281/zenodo.7044924
Owner
- Name: Austin Hovland
- Login: Austin-s-h
- Kind: user
- Location: Boston, MA
- Twitter: AustinHovland
- Repositories: 1
- Profile: https://github.com/Austin-s-h
PhD | Bioinformatician and Molecular Biologist | Single Cell Genomics, Custom NGS Analysis, Long Read Transcriptomics. | D&D, Web3, Computer Hardware, Dogs