GEO2R: compare two or more groups of Samples
GEO2R to compare two or more groups of Samples in order to identify genes that are differentially expressed across experimental conditions.1284 days ago
StringTie Transcript assembly and quantification for RNA-Seq
...reads that can also be used by other transcript assemblers, but also alignments of longer sequences that have been assembled from those reads. In order to identify differentially ex...1478 days ago
LibsDyogen: Libibrary for comparative genomics
Library of usual classes and functions written in python and used in the Dyogen team for comparative genomics applications. Collaborative python library used in the DYOGEN teamfor studying the evolution of gene order in vertebrates. http://www.ibens.ens.fr/?rubrique43&lang=fr1645 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
...eClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large...1636 days ago
RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
...software Phrap is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. The u...1635 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
glia's main use is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM alignments.&nb...1611 days ago
1591 days ago
CSAR-web: a web server of contig scaffolding using algebraic rearrangements
CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomple...1538 days ago
URMAP, an ultra-fast read mapper
URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calli...1335 days ago
Platypus – R package for object detection and image segmentation.
...ll the latest version of platypus with remotes package: remotes::install_github("maju116/platypus") Note that in order to install platypus ...1325 days ago