Version 2.2.4

Update and fix cut & run cli

Version 2.2.3

• Fix problems with multiqc pulling in enhancer plot
• Fix file path issue with deeptools_gene_all
• Updated annotations for hg38 and mm10

Version 2.2.2

• chore: moved FRiP and jaccard rules to peakqc.smk
• fix: bug in FRiP_SEACR rule
• docs: improved documentation regarding blocking

Version 2.2.1

• verification of auto release from fork

Version 2.2.0

MultiQC report revamp

• Update of multiQC version used to v1.32 via sif container
• Complete recreation of the multiQC yaml in references (changes include splitting modules, changing flow, and adding manual descriptions)
• Addition to multiQC report of: Encode QC metrics, interactive enhancer profile plots (when created), interactive Spearman correlation plot, interactive TSS profile plots
• Also includes a minor bug fix so that DiffBind_QC rules do not rerun every run of the pipeline

Continuous Integration

• Adding multiple CI components to harden pipeline
  • check version
  • auto release
  • snakevis on release

v2.1.0

What's Changed

• feat: Adding new summary tables of QC stats by @rroutsong in #100
• feat: Adding mm39 reference genome by @rroutsong @tovahmarkowitz in #102
• docs: Adding docs for manually running DiffBind outside of pipeline by @rroutsong @tovahmarkowitz in #94
• fix: Bug fixes by @rroutsong in #103 #104 #105

Full Changelog: v2.0.0...v2.1.0

v2.0.0

What's Changed

New features:

• FRiP plotting
• DiffBindQC report (DiffBind-based peak calling comparison across samples)
• TPM counts of consensus peaks for external differential peak calling
• Deeptools plots: spearman correlation, pearson correlation, PCA, fingerprint plot,
  metagene plots, TSS plots, enhancer plots
• Addition of the cutnrun assay with SEACR
• Homer for motif calling
• Jaccard calculation
• Merged table of differential peak table and uropa finalhits output

Improvements

• DiffBind differential peak calling reorganization and improved html reports
• Separation of PE and SE rules
• Encode QC metric calculation on PE data without requirement of ppqt
• Improved documentation
• Improvements to peakcall file parsing and new column names
• Addition of peakcall file highlighting to make error checking easier
• Expanded rerun triggers

Full Changelog: v1.2.0...v2.0.0

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