Kmer: a suite of tools for DNA sequence analysis
More at https://help.rc.ufl.edu/doc/Kmer This also includes: A2Amapper: ATAC, Assembly to Assembly Comparision tool: Comparative mapping between two genome...1019 days ago
1019 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.1013 days ago
k-mers tutorial - classification and taxonomy
DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, ...1010 days ago
989 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 w...966 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, miRNA...886 days ago
oGNM:Conformational dynamics based on contact topology in a coarse-grained presentation
Gaussian Network Model (GNM) is a powerful tool to sample conformational dynamics based on contact topology in a coarse-grained presentation. Here we present a method t...867 days ago
odgi: optimized dynamic genome/graph implementation
odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analys...851 days ago
821 days ago