Supplementary Material for Journal Articles

Data and code for:
Bediaga et al (2021)
Cytotoxic CD4+ T cells are markers of progression to type 1 diabetes.
Submitted

Data and code for:
Chen Y, Pal B, Visvader JE, & Smyth GK (2017)
Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR.
F1000Research

Data and code for:
Chen Y, Lun ATL, & Smyth GK (2016)
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.
F1000Research 5, 1438.

Supplementary Information for:
Lun ATL, Chen Y, & Smyth GK. (2016)
It's DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR.
Methods in Molecular Biology, 1418, 391-416.

Supplementary Information for:
Lun ATL, & Smyth GK. (2015)
csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows
Nucleic Acids Research 44, e45.

Supplementary Information for:
Chen Y, Lun ATL, & Smyth GK. (2014)
Differential expression analysis of complex RNA-seq experiments using edgeR.
Statistical Analysis of Next Generation Sequence Data, Springer, New York, pages 51-74.

Supplementary Information for:
Law CW, Chen Y, Shi W & Smyth GK. (2014)
Voom! Precision weights unlock linear model analysis tools for RNA-seq read counts.
Genome Biology 15, R29.

Supplementary Information: Normalization for digital gene expression (e.g. RNA-seq) data
Robinson MD and Oshlack A
A scaling normalization method for differential expression analysis of RNA-seq data
Genome Biology 2010, 11:R25. [PubMed Abstract]

FIRMAGene R package for using Affymetrix Gene 1.0ST arrays to detect differential splicing events.
Robinson MD and Speed TP
Differential splicing using whole-transcript microarrays.
BMC Bioinformatics 2009, 10:156 [PubMed Abstract]

Supplementary Information: Differential Expression for DGE data
Referenced by:
Robinson MD and Smyth GK. (2007)
Moderated statistical tests for assessing differences in tag abundance.
Bioinformatics.

Supplementary Information: Background Correction for microarrays
Referenced by:
Ritchie ME, Silver, J., Oshlack A, Holmes M, Diyagama D, Holloway A & Smyth GK. (2007)
A comparison of background correction methods for two-colour microarrays.
Bioinformatics 23(20):2700-2707 [PubMed Abstract].

Data files: Boutique Array Normalization
From the paper:
Oshlack A, Emslie D, Corcoran L, & Smyth GK.
Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes
Genome Biology 2007, 8:R2 [Full Text].

Supplementary Information: Mixture
Referenced by:
Holloway AJ, Oshlack A, Diyagama DS, Bowtell DDL & Smyth GK.
Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

Supplementary Information: arrayWeights
Referenced by:
Ritchie ME, Diyagama D, Neilson J, van Laar R, Dobrovic A, Holloway A & Smyth GK. (2006)
Empirical array quality weights in the analysis of microarray data.
BMC Bioinformatics 7, Article 261. [PubMed Abstract] [Publisher Full Text]

Supplementary materials for:
Smyth, G. K., Michaud, J., and Scott, H. (2005).
The use of within-array replicate spots for assessing differential expression in microarray experiments.
Bioinformatics 21 (9), 2067-2075.

Marcoil Homepage
Referenced by:
Delorenzi M, Speed T.
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.
Bioinformatics. 2002 Apr;18(4):617-25.

Phat Homepage
Referenced by:
Cawley SE, Wirth AI, Speed TP.
Phat--a gene finding program for Plasmodium falciparum.
Mol Biochem Parasitol. 2001 Dec;118(2):167-74.