Admin: Getting started * Setting up an analysis * Data Management * Reproducible Research * Methods for manuscripts * Downloading data * Globus * 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 * FASRC * 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 * Nextflow bulk RNA-Seq alignment on fas.rc QuickStart guide

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 * single-cell pseudobulked sample size power analysis * Subclustering and iteration policy

Spatial Transcriptomics: Running Baysor on o2 * Baysor Output into a Seurat Object

Training Team: GitHub page * Training Webpage * Workshop materials * HTML reference for GitHub-flavored Markdown * GitHub Pages Documentation

• Team members: Will Gammerdinger, Elizabeth Partan, Noor Sohail, Shannan Ho Sui
• Email: hbctraining (at) hsph.harvard.edu

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

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How it is organized

• minimal overhead: feel free to add any piece of knowledge in any way
• easy to navigate in one click
• github is tracking changes for you
• it is ok to have multiple similar recipes
• growing naturally
• no placeholders
• please name all pages in small_letters.md
• order matters: topics come alpabetically, but within topic and within page please put important things first (important articles/tools on top, important links on the left).

How to contribute

• nagivate to where you want to share your knowledge or fix something
• don’t create a new folder unless you have >=2 new pages that don’t fit into existing structure
• add actual value (know how), not structure
• hit ‘edit file’ or ‘new file’ (add .md extension)
• translate knowledge from your mind into markdown
• hit ‘preview changes’ to make sure your formatting is fine
• hit ‘commit changes’
• thank you, you just have saved somebody’s day!

Knowledge we need to extract (aka TODO):

• ATAC-seq
• miRNA
• integrate (link?) hbctraining, tutorials, bcbio docs
• https://github.com/hbc/hbcABC
• https://github.com/vbarrera/bcbioLite
• Lorena’s wisdom:
  • information that apply to all templates: http://bioinformatics.sph.harvard.edu/hbcABC/articles/general_start.html
  • List of templates right now: http://bioinformatics.sph.harvard.edu/hbcABC/articles/list_of_templates.html
  • single cell custom templates: http://bioinformatics.sph.harvard.edu/hbcABC/articles/singlecell-tutorial.html
• Victor’s wisdom:
  • Containerization and automated setup of Docker or Conda envs for a project
  • Singularity on O2
  • Running nf-core pipelines on O2