Pinned Repositories
aifi-swanson-teaseq
Code related to Swanson, et. al. for TEA-seq, ICICLE-seq, and scATAC-seq data processing, analysis, and visualization
analysis-workflows
Open workflow definitions for genomic analysis from MGI at WUSM.
AnnotationHub
Client for the Bioconductor AnnotationHub web resource
atac-seq-pipeline
ENCODE ATAC-seq pipeline
awesome-10x-genomics
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
awesome-cancer-variant-databases
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
awesome-multi-omics
List of software packages for multi-omics analysis
awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
bam-readcount
count DNA sequence reads in BAM files
bfx-workshop
procha2's Repositories
procha2/hpc-intro
Practical course on running jobs on a HPC
procha2/ENCODE-cCREs
Pipelines to create and analyze ENCODE candidate cis-Regulatory Elements
procha2/Intro-to-ChIPseq
Intro to ChIPseq using HPC
procha2/R_notes
Data science in R notes
procha2/MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics
procha2/tximport
Import and summarize transcript-level estimates for gene-level analysis
procha2/SNP_notes
Notes on SNP-related tools and genome variation analysis
procha2/tximeta
Transcript Quantification Import with Automatic Metadata
procha2/dataviz-figdesign
Introduction to Figure Design and Data Visualisation with ggplot2
procha2/Statistics_notes
Statistics, data analysis tutorials and learning resources
procha2/ensembldb
This is the ensembldb development repository.
procha2/Immuno_notes
Immunology-related bioinformatics data and tools
procha2/Conference_notes
Notes on potential conferences
procha2/SC3
A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
procha2/Grants_notes
Notes on potential funding opportunities
procha2/AnnotationHub
Client for the Bioconductor AnnotationHub web resource
procha2/MDnotes
Links to all data science, genomics, and other notes
procha2/comp-bio-setup
Set up a computer for Computational Biology
procha2/sc3s
Single Cell Consensus Clustering with Speed
procha2/shell-genomics-remote
Introduction to the Command Line for Genomics
procha2/sc-school-2021
procha2/scATACseq-analysis-notes
my notes for scATACseq analysis
procha2/cellranger-atac
procha2/rna-seq-pipeline
procha2/users-meeting-2020-workshop
procha2/DataScienceSchool
procha2/genomic-data-client
procha2/qc-utils
QC infrastructure common to several pipelines
procha2/dna-me-pipeline
DCC/DAC methylation pipeline source
procha2/Workshop_Annotation
Course materials for "Variants Annotate and Phenotype Analysis"