What I offer

The following list is preliminary and will be expanded in the future.

Raw Data Quality Control

FastQChttps://www.bioinformatics.babraham.ac.uk /projects/fastqc/

RNA sequencing analysis

Tuxedo Suite Gosh S and Chan CK, Analysis of RNA-Seq Data Using TopHat and Cufflinks., Methods Mol Biol. 2016;1374:339-61
STAR-aligner (TCGA pipeline) Dobin A, et al, STAR: ultrafast universal RNA-seq aligner., Bioinformatics.2013 Jan; 29(1): 15–21.
HiSAT2 aligner Kim D et al, HISAT: a fast spliced aligner with low memory requirements., Nat Methods. 2015 Apr;12(4):357-60.

…and others upon request

ATACseq analysis

Pipeline described by Buonrostro et al.Buenrostro J, et al, Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position., Nat Methods. 2013 Dec;10(12):1213-8.


…in preparation

Differential analysis (genes, peaks)

DESeq, DESeq2, EdgeR and others upon request

Illumina Infinium450k and EPIC microarrays

Minfi pipelineAryee et al, Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays., Bioinformatics. 2014 May 15;30(10):1363-9.

additional analyses

Heatmaps, PCA, tSNE, hierarchical clustering, consensus clustering etc.