Tutorials - Statistical Genomics Foundry

Tutorials

Faithful research notes on tool vignettes and tutorials — recommended procedure, exact defaults, and short load-bearing quotes, each pinned to the version summarized and linked to the original. Not reproductions.

1.52.0

DESeq2 vignette — "Analyzing RNA-seq data with DESeq2"

Love MI, Anders S, Huber W. Analyzing RNA-seq data with DESeq2 — Bioconductor package vignette, DESeq2 v1.52.0. License LGPL (>= 3) per the DESeq2 Bioconductor landing page. Methods: Love, Huber & Anders, Genome Biology 2014;15:550.
0.5.0

designit: Blocking and Randomization for Experimental Design

designit: Blocking and Randomization for Experimental Design, version 0.5.0 (published 2024-03-21). Davydov I, Siebourg-Polster J, Steiner G, Rudolph J, Zhang JD, Banfai B. © F. Hoffmann-La Roche, MIT licensed. https://cran.r-project.org/package=designit — read from the CRAN source tarball (DESCRIPTION, NAMESPACE, R/, vignettes, inst/doc).
hisse 2.1.11

hisse vignette — "Type I errors, Model rejection, & HiSSE vs. FiSSE"

Beaulieu JM. Type I errors, Model rejection, & HiSSE vs. FiSSE. hisse package vignette, rendered 2023-02-16; version pinned from CRAN hisse v2.1.11 in the source note. Rendered vignette and companion Rmd consulted.
limma: Linear Models for Microarray and Omics Data — package documentation

Gordon K. Smyth et al., limma (Bioconductor). Package version 3.68.4. Licensed GPL (>=2).
1.60.0

OSAT — "An introduction to OSAT" (Bioconductor vignette + reference manual)

Li Yan (author/maintainer). OSAT: Optimal Sample Assignment Tool, Bioconductor package v1.60.0 (Bioconductor 3.23). Vignette "An introduction to OSAT" by Li Yan, Changxing Ma, Dan Wang, Qiang Hu, Maochun Qin, Jianmin Wang, Song Liu. Licensed Artistic-2.0 per the package DESCRIPTION and the Bioconductor landing page. Related paper: http://www.biomedcentral.com/1471-2164/13/689
4.10.8

PAML Manual — codeml ancestral reconstruction + codon positive selection

Yang Z. PAML Manual, version 4.10.8, November 2024. Manual bundled with the PAML software package and distributed under GNU GPL v3 per the source note. Package citation: Yang Z. PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24:1586-1591, 2007.
1.36.0

RNA-seq workflow: gene-level exploratory analysis and differential expression (rnaseqGene)

Michael I. Love, Simon Anders, Vladislav Kim, Wolfgang Huber. rnaseqGene Bioconductor workflow package, version 1.36.0 (Bioconductor 3.23). Licensed Artistic-2.0. https://bioconductor.org/packages/release/workflows/html/rnaseqGene.html — read from the rendered vignette HTML; an F1000Research version exists (DOI 10.12688/f1000research.7563.1) and is stated to differ.
3.60.0

The SVA package for removing batch effects and other unwanted variation in high-throughput experiments

sva: Surrogate Variable Analysis, version 3.60.0 (Bioconductor 3.23). Leek JT, Johnson WE, Parker HS, Fertig EJ, Jaffe AE, Storey JD, Zhang Y, Collado-Torres L. Artistic-2.0. https://bioconductor.org/packages/release/bioc/html/sva.html — signatures and defaults read off the reference manual (the vignette prints call sites only).