1423 days ago
RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
...transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-end bulk RNA-seq (strand-specific/agnostic) paired-end single-cell RNA-seq (strand-specific/agnostic) n...1401 days ago
SEASTAR: Systematic Evaluation of Alternative STArt site in RNA
...TArt site in RNA) is a software package for Transcription Start Site (TSS) identification and quantification using only RNA-seq data. It assembles novel TSSs based only on RNA-Seq data and merges them with kno...1366 days ago
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 promoter a...1366 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...1262 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 TF...1261 days ago
Applied Computational Genomics Course at UU: Spring 2020
...ncing technologies will be explored including sequence alignment, the identification of genetic variation, structural variation, and ChIP-seq and RNA-seq analysis. Students will learn...1234 days ago
1204 days ago
IVA: accurate de novo assembly of RNA virus genomes
IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 seque...1052 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.991 days ago