v1.2.0

What's Changed

• Major refactor codebase by @rroutsong in #41
• Added time stamp to slurm out and err logs by @rroutsong in #42
• Removal of MEME and SICER due to issues in the previous version
• UROPA now only runs protTSS option

New Contributors

• @rroutsong Made their first contribution 🎉 in #41

Full Changelog: v1.1.0...v1.2.0

v1.1.0

What's Changed

• Update Snakefile by @tovahmarkowitz in #30
• add blocking to the diffbind csv prep by @tovahmarkowitz in #35
• Adding new DiffBind QC Rmd for cfChIP and a few other DiffBind updates by @tovahmarkowitz in #36
• Adding new DiffBindQC for cfChIP by @tovahmarkowitz in #37
• Adding memory for diffbind jobs by @tovahmarkowitz in #38
• Updates to CI include every major permutation of running the ChIP-, cfChIP-, and ATAC-seq pipelines @skchronicles
• Updates to documentation to include FAQ and description/overview of pipeline and its different types of output files @tovahmarkowitz @skchronicles
• Re-building cfChIP docker image to include additional R packages @skchronicles
• Adding MEME to pipeline @tovahmarkowitz
• Adding spearman heatmap and PCA plots @tovahmarkowitz
• Updates to handle single-end data @tovahmarkowitz
• Updates to handle ChIP-seq data/processing lacking input control samples @tovahmarkowitz

Full Changelog: v1.0.2...v1.1.0

v1.0.0

chrom-seek (v1.0.0)

This is the first major release of the chrom-seek pipeline! chrom-seek is an awesome set of epigenetic pipelines designed to process and analyze paired-end cell-free ChIP-seq, ChIP-seq, and ATAC-seq data.

Contributors

A big thanks to the contributors who made this release possible:

• @tovahmarkowitz, @asyakhl, @skchronicles

Cite

If you use this software, please cite our methods paper:

BibText

@article {Jange202302003,
	author = {Moon Kyoo Jang and Tovah E Markowitz and Temesgen E Andargie and Zainab Apalara and Skyler Kuhn and Sean Agbor-Enoh},
	title = {Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation},
	volume = {6},
	number = {12},
	elocation-id = {e202302003},
	year = {2023},
	doi = {10.26508/lsa.202302003},
	publisher = {Life Science Alliance},
	abstract = {Existing monitoring approaches in heart transplantation lack the sensitivity to provide deep molecular assessments to guide management, or require endomyocardial biopsy, an invasive and blind procedure that lacks the precision to reliably obtain biopsy samples from diseased sites. This study examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) as a noninvasive proxy to define molecular gene sets and sources of tissue injury in heart transplant patients. In healthy controls and in heart transplant patients, cfChIP-seq reliably detected housekeeping genes. cfChIP-seq identified differential gene signals of relevant immune and nonimmune molecular pathways that were predominantly down-regulated in immunosuppressed heart transplant patients compared with healthy controls. cfChIP-seq also identified cell-free DNA tissue sources. Compared with healthy controls, heart transplant patients demonstrated greater cell-free DNA from tissue types associated with heart transplant complications, including the heart, hematopoietic cells, lungs, liver, and vascular endothelium. cfChIP-seq may therefore be a reliable approach to profile dynamic assessments of molecular pathways and sources of tissue injury in heart transplant patients.},
	URL = {https://www.life-science-alliance.org/content/6/12/e202302003},
	eprint = {https://www.life-science-alliance.org/content/6/12/e202302003.full.pdf},
	journal = {Life Science Alliance}
}

APA

Jang, M. K., Markowitz, T. E., Andargie, T. E., Apalara, Z., Kuhn, S., & Agbor-Enoh, S. (2023). Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation. Life Science Alliance, 6(12), e202302003. https://doi.org/10.26508/lsa.202302003