Project Description
GoPeaks Window-based peak caller written in Go for CUT&TAG data. Shout out to jakevc for writing most of it!
CUT&TAG Align reads, call peaks, and find differential peaks across all unique combinations of conditions in CUT&TAG data.
GoPeaks-Compare* Benchmark GoPeaks with peak callers MACS2 and SEACR for CUT&TAG data [Insert DOI].
ATAC-Seq* Find differential open-chromatin regions between all unique combinations of conditions in paired-end ATAC-Seq data. Both DiffBind and default DESeq2 are used in case some experiments do not fit DESeq2’s assumptions (e.g. global change in ATAC signal).
CITE-Seq* Import output of CellRanger into this secondary analysis pipeline to assess quality control, integrate samples together, cluster with UMAP, and test for differential expression + GO with various schemes.
RNA-Seq Assess differential gene expression in RNA-Seq data. Shout out to JEstabrook for writing most of it!
HINT-ATAC* Implementation of HINT-ATAC by Zhijian, Li et. al. to find transcription factor footprints in ATAC-Seq data. This is deprecated.

In addition to work-related projects, I try to contribute work to open-source projects like:

Project Description
MultiQC GoPeaks Parse the output log file for GoPeaks to display peak counts per sample to the user.
MultiQC Sambamba MarkDup Calculate duplication rate for paired and single-end sequencing libraries.
HINT-ATAC Fixed sequencing depth normalization problems for ATAC-Seq footprinting.

*Most of this project was written by me.

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