proActiv: Estimation of Promoter Activity from RNA-Seq data
proActiv is an R package that estimates promoter activity from RNA-Seq data. proActiv uses aligned reads and genome annotations as input, and provides absolute and relative...1375 days ago
DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms
DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or fro...1270 days ago
MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs an...1270 days ago
Applied Computational Genomics Course at UU: Spring 2020
This course will provide a comprehensive introduction to fundamental concepts and experimental approaches in the analysis and interpretation of experimental genomics data....1243 days ago
1212 days ago
RNA-Seq differential expression work flow using DESeq2
One of the aim of RNAseq data analysis is the detection of differentially expressed genes. The package DESeq2 provides methods to test for differential expression analysis.1000 days ago
975 days ago
RNA-seq workflow: gene-level exploratory analysis and differential expression
Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were...953 days ago
ChIPBase: open database for studying the transcription factor binding sites and motifs
ChIPBase v2.0 is an open database for studying the transcription factor binding sites and motifs, and decoding the transcriptional regulatory networks of lncRNAs, miRNAs, o...872 days ago