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/atac-seq-pipeline
ENCODE ATAC-seq pipeline
procha2/bioconda-recipes
Conda recipes for the bioconda channel.
procha2/Bite-size-R-v2
CRUK-CI Bite-size R course
procha2/Bitesize_SingleCell
April - May 2022
procha2/Bulk_RNAseq_Course_Base
procha2/Bulk_RNASeq_Course_March23
Course repo for March 2023
procha2/Bulk_RNAseq_Course_Nov22
Nov - Dec 22
procha2/chip-seq-pipeline2
ENCODE ChIP-seq pipeline
procha2/chromhmm-pipeline
WDL pipeline for chromhmm
procha2/dnase-seq-pipeline
ENCODE DNase-seq pipeline
procha2/experimental-design
A Course on designing high-throughput experiments
procha2/IntroductionToStats
Refresher training course on the foundations of statistical analysis. http://tinyurl.com/cruk-stats
procha2/linear-models-r
Going beyond the t-test in R and introducing linear regression and ANOVA (http://tinyurl.com/linear-models-r)
procha2/long-read-rna-pipeline
ENCODE long read RNA-seq pipeline
procha2/Managing-your-research-data
Course on good principles & practices in Data Management (https://tinyurl.com/cruk-myrd)
procha2/metabolomics2018
Workshop for the xcms(3) workshop at the metabolomics 2018 conference in Seattle
procha2/mirna-seq-pipeline
procha2/nextflow_september_2021
procha2/PHD-Dataskills
CRUK PhD Dataskill session (https://tinyurl.com/dataskillz)
procha2/Quantitative-ChIPseq-Workshop
EuroBioc 2020 Workshop: ChIP and ATAC analysis with DiffBind
procha2/r-intro-1
R training course during the coronavirus lockdown
procha2/regulome-encoded
Temp repo for regulome development
procha2/scg_lib_structs
Collections of library structure and sequence of popular single cell genomic methods
procha2/scRNA-seq_online
procha2/sentieon-google-genomics
Run Sentieon pipelines on Google Cloud Platform
procha2/SingleCell_RNASeq_May23
procha2/UnivCambridge_ScRnaSeqIntro_Base
procha2/UnivCambridge_ScRnaSeqIntro_Feb2022
procha2/UnixIntro
procha2/wgbs-pipeline
ENCODE whole-genome bisulfite sequencing (WGBS) pipeline