Admin: Getting started Setting up an analysis Data Management Reproducible Research Methods for manuscripts Downloading data Acknowledging funding Initial consults Chargeback models Archiving project folders Consulting resources Pull for knowledge work instead of push Scripts for tracking storage on O2
RC: O2 OpenPortal Connection to HPC Keep command alive IPython notebook Manage files O2 tips Scheduler Jupyter notebooks tmux tips FAS virtual desktopsArrays in SlurmCommon O2 portal Issues
bcbio: docs issues validation running in parallel genomes tips RNA-seq workflow by Mary installation by Michael installation by Sergey RNA-seq workflow by Systems Pharmacology lab gtf/gff validators Create hybrid mammal virus genome python package in 2022
Bulk RNA-seq: Count normalization methods Dexseq Failure types IRFinder_report RepEnrich2 guide IRFinder Strandedness Tools Bibliography Bibliography.bib ASE eQTL GTEx SummarizedExperiment templates for QC and DE analyses bcbioLite Cluster profiler ggsashimi Differential exon usage with Suppa2 cell type deconvolution webgestalt Differential splicing with Leafcutter
CHIP-seq: ENCODE Guidelines CHIp-seq intro Tools Cut&RUN Antibody column on metadata Cut&RUN for tfBS Cut&Run tools2 * TF regulons
Misc: Git tips Organized papers AWS Core resources General NGS Orphan improvements OSX Snakemake miRNA detect sample mislabeling Get SRA links GNU parallel GEO Submissions Report FAQs Snippet teaching materials from Liu lab Connected papers Speciation genomics tutorial Custom Genome with Reform Multiomics Factor Analysis Bioinformatics course BARC SOP - WI MIT Babraham courses Illumina Dragen JTLeek group genomics papers R-Metabolomics Nextflow training IOWA State U bioinformatics core knowledgebase Long-read presentation from Jihe Creative science bioinformatics tutorials NCI Bioinformarics workbook
Nanopore: Master of pores from CRG Tombo Megalodon * Processing Direct RNA Sequencing data on O2
Multi-omics integration: Diablo paper vignette * totalVI - citeSeq
R: .Rprofile RShiny htmlwidgets Tip and tricks Complex heatmap Fundamentals of data visualization Big Book of R Statistical rethinking and other bookdown books Boxplot evolution Intro to stat computing data to viz modern statistics for modern biology Heatmap examples Learniing statistics with R Understanding statistics and experimental design data analysis and prediction algorithms with R R for data analysis Exclude ranges * R crash course
Python: Conda on O2
Single Cell RNA-seq: Bcbio indrops3 Rstudio docker Saturation Clustering analysis in Seurat Seurat markers Single Cell conda Cell types Tools Tutorials Bibliography Velocity Doublets Zinbwaver pseudobulk DESeq2 pseudobulk edgeR CITE-seq Library structures Seurat to 10X counts Azimuth Running Cell Ranger O2 Cluster annotation tutorial Diff composition analysis OSCA upstream TF with pySCENIC SC article list for beginners demuxafy (includes demultiplexing, background and doublet detection tools Lymphocyte Antigen Receptor Transcripts and Clustering DoubletFinder Running Mast * Publication Quality UMAPs
Training team: github Upcoming workshops Past workshops * Workshop materials
Variants: Clonal evolution Cancer variant databases Open Cravat Applied computational genomics course by A. Quinlan SC Phylogeny Validating variants in IGV Human Genome Variation Lab
WGS: CRISPR offtarget * Pacbio genome assembly
WGBS: BCratio using centromere as spike-in * RnBeads