Pinned Repositories
2021-04-26-umich-rnaseqDemystified
RNA-Seq Demystified workshop
2021-11-15-umich-rnaseq-demystified
Fall 2021 RNAseq Demystified Workshop
2022-02-28-umich-computational-foundations
https://umich-brcf-bioinf.github.io/2022-02-28-umich-computational-foundations/html
Connor
Deduplication based on custom inline DNA barcodes.
GeneRollup
Command-line tool that accepts a TSV file of variants by samples and emits an XLSX file of genes by samples, rolling up one or more variants into a single gene row.
Jacquard
Suite of command-line tools to expedite analysis of exome variant data from multiple patients and multiple variant callers.
Katana
Command-line tool to soft-clip reads based on primer locations.
single_cell_env
An environment for single-cell RNAseq
Watermelon
RNA-Seq NGS Pipeline
Zither
Command-line tool to pull raw depths and alt freqs from BAM file(s) based on an existing VCF, writing output as new VCF to stdout.
UM BRCF Bioinformatics Core's Repositories
umich-brcf-bioinf/Watermelon
RNA-Seq NGS Pipeline
umich-brcf-bioinf/2021-04-26-umich-rnaseqDemystified
RNA-Seq Demystified workshop
umich-brcf-bioinf/single_cell_env
An environment for single-cell RNAseq
umich-brcf-bioinf/2021-11-15-umich-rnaseq-demystified
Fall 2021 RNAseq Demystified Workshop
umich-brcf-bioinf/2022-02-28-umich-computational-foundations
https://umich-brcf-bioinf.github.io/2022-02-28-umich-computational-foundations/html
umich-brcf-bioinf/2021-08-09-umich-rnaseq-demystified
Repository for Summer 2021 RNASeq Demystified Workshop materials
umich-brcf-bioinf/2021-10-18-UM-SWC-Lessons
Custom curriculum for teaching R, the Unix Shell, & Git with an integrated workflow and reproducible research practices.
umich-brcf-bioinf/2022-03-14-umich-rnaseq-demystified
umich-brcf-bioinf/2022-07-25-umich-computational-foundations
umich-brcf-bioinf/2022-08-08-umich-rnaseq-demystified
umich-brcf-bioinf/2022-10-31-umich-computational-foundations
Computational Foundations Workshop Lessons
umich-brcf-bioinf/2022-11-14-umich-rnaseq-demystified
RNA-Seq Demystified workshop lesson plans
umich-brcf-bioinf/2023-02-27-umich-computational-foundations
Computational Foundations Workshop Lesson Plans
umich-brcf-bioinf/2023-03-13-umich-rnaseq-demystified
RNA-Seq Demystified Workshop Lesson Plans
umich-brcf-bioinf/2023-05-07-umich-r-studio-revealed
R/R-Studio Workshop lesson plans
umich-brcf-bioinf/2023-07-31-umich-computational-foundations
Computational Foundations Workshop Lessons
umich-brcf-bioinf/2023-08-14-umich-rnaseq-demystified
umich-brcf-bioinf/analysis_workflows
Brief methods for common analyses
umich-brcf-bioinf/boat
umich-brcf-bioinf/fastp
Environment with fastp
umich-brcf-bioinf/geomx_env
An environment for GeoMX tools
umich-brcf-bioinf/macs2
umich-brcf-bioinf/multiqc
umich-brcf-bioinf/proteomics_env
umich-brcf-bioinf/python3_pandas_excel
Environment with python3, pandas, and several libraries for manipulating excel docs
umich-brcf-bioinf/rsem_star
Environment with rsem and star
umich-brcf-bioinf/WAT_diffex
Environment for Watermelon's differential expression steps
umich-brcf-bioinf/workshop-computational-foundations
umich-brcf-bioinf/workshop-intro-single-cell
Intro to Single Cell Workshop lesson plans
umich-brcf-bioinf/workshop-rnaseq-demystified