StringTie Transcript assembly and quantification for RNA-Seq
...cript assemblers, but also alignments of longer sequences that have been assembled from those reads. In order to identify differentially expressed genes between experiments, StringTi...1439 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
...ral adjacencies, namely DeCo, DeCoLT, ART-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission e...1597 days ago
alien_index : identify potential contaminants or horizontally transferred genes in transcriptomes.
identify potential contaminants or horizontally transferred genes in transcriptomes. algorithm is based on alogorithm described in the following: Gladyshev, Eugene A., Matthew Mesel...1567 days ago
PANEV: an R package for a pathway-based network visualization
...rk visualization. Based on information available on KEGG, it visualizes genes within a network of multiple...ph visualization helps to interpret functional profiles of a cluster of genes. https://bmcbioinformatics.b...1560 days ago
1533 days ago
ShinyGO v0.61: Gene Ontology Enrichment Analysis + more
...2031 genomes (including bacteria and fungi) are annotated based on STRING-db (v.10). In addition, it also produces KEGG pathway diagrams with your genes highlighted, hierarchical clu...1445 days ago
ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome b...1404 days ago
1374 days ago
SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
...cedures. Thus, SqueezeMeta features several unique characteristics: Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome Co-assemb...1370 days ago
MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
...atistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without an a priori binary classification of genes as targets or non-targets. Wh...1269 days ago