| 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.
Projects are ranked from newest to oldest