CLARK is a software tool for classifying any type of DNA/RNA sequences

Analyzing and Modeling Time Series Gene Expression with STEM and DREM

Transcription factor–DNA binding: beyond binding site motifs

HarvardX Biomedical Data Science Open Online Training

Genome-wide methylation data mirror ancestry information

novel method developed within the MAQC-III project utilizing the expression distributions, corrected for noise and batch effects, and assisted by random resampling, to compute DEG scores related to the Wilcoxon U test (Magic, see Additional file 1: Supplementary Note 2)

MOSAiCS implements a model-based approach where the background distribution for unbound regions take into account systematic biases such as mappability and GC content and the peak regions are described with a two component Negative Binomial mixture model

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

Robust enumeration of cell subsets from tissue expression profiles

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

CIBERSORT, a computational approach for inferring leukocyte representation in bulk tumor transcriptomes

SomaticSniper

Salmon provides fast and bias-aware quantification of transcript expression

KaryoStudio

argyle: An R Package for Analysis of Illumina Genotyping Arrays

RCP: a novel probe design bias correction method for Illumina Methylation BeadChip

The ISMARA client

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

I'm the developer of pyGeno. Here's a little script that does just that for the Gene TPST2, by using segment trees

Voyant Tools is a web-based reading and analysis environment for digital texts.