ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomi...It is designed to be user-friendly, and has been optimized for speed...sp;for installation, a user's guide, and examples. https://journals.plos.org/ploscompbiol/article?...1503 days ago
QuartataWeb: user-friendly server developed for polypharmacological and chemogenomics analyses.
Data on protein-drug and protein-chemical interactions...ses such as DrugBank and STITCH. These data usual...nt studies, both computational and experimental, highlighted the...ose known in public databases; and many proteins bind chemicals...oup.com/bioinformatics/advance-article/...1489 days ago
wgd—simple command line tools for the analysis of ancient whole-genome duplications
wgd is a easy to use command-line tool for KS distributio...te provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering thes...ttps://academic.oup.com/bioinformatics/article/...1376 days ago
Updated science-wide author databases of standardized citation indicators
There was great interest in the databases of standardized citation metrics across all scientists and scientific disciplines [1], and many sci...l the end of 2019 (Table-S6-career-2019) and for citation impact during th...data.mendeley.com/datasets/btchxktzyw/2, and any...1260 days ago
Pandoc: The universal markup converter
Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. Pandoc is a free and open-source document converter, widely used as a writing tool and as a basis for publishing workflows. More at https://pandoc.org/1197 days ago
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/61467721142 days ago
LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo as...s, an approach that has been successful with short reads. https://academic.oup.com/ve/article/...1041 days ago
QuasiModo - Quasispecies Metric Determination on Omics
This repository contains the scripts and pipeline that reproduces the results...study we evaluated genome assemblers and variant callers on 10 in vitr...n also be used to evaluate assemblies and variant calling results on ot...tasets. https://academic.oup.com/bib/article/...1038 days ago
k-mers tutorial - classification and taxonomy
DNA k-mers underlie much of our assembly work, and we (along with many others!) have sp...iently, discard redundant data, and count them efficiently....k-mer based similarity measures and computing and searching...a little bit of a literature review and waxi...977 days ago
PaReBrick: PArallel REarrangements and BReaks identification toolkit
PaReBrick. The tool takes a collection of s...uence of oriented synteny blocks and a phylogenetic tree as input...hem for consistency with a tree, and sorts the events by their par...red blocks or their extra copies and the inversions in which copie...c.oup.com/bioinformatics/advance-article/...934 days ago