Tools   Select Another Resource Report Type

https://github.com/elsevierlabs-os/spark-xml-utils

Software library to filter documents based on XPath expression, return specific nodes for XPath/XQuery expression, transform documents using XSLT stylesheet. By providing some basic wrappers to Saxon, spark-xml-utils library exposes some basic XPath, XQuery, and XSLT functionality that can readily be leveraged by any Spark application.

Proper citation: spark-xml-utils (RRID:SCR_023635) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-EUtilities

Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic.

Proper citation: Bio-EUtilities (RRID:SCR_024064) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Tools-Run-Alignment-Clustalw

Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.

Proper citation: Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/tab2mage/

Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.

Proper citation: Tab2MAGE (RRID:SCR_024101) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Tools-Phylo-PAML

Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.

Proper citation: Bio-Tools-Phylo-PAML (RRID:SCR_024069) Copy   

•   Source: SciCrunch Registry

http://colibread.inria.fr/software/mapsembler2/

Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.

Proper citation: Mapsembler2 (RRID:SCR_024102) Copy   

•   Source: SciCrunch Registry

https://github.com/gerddie/maxflow

Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph.

Proper citation: MAXFLOW (RRID:SCR_024103) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Graphics

Software package to generate GD images of Bio::Seq objects.

Proper citation: Bio-Graphics (RRID:SCR_024061) Copy   

•   Source: SciCrunch Registry

https://github.com/genouest/biomaj-cli

Software package to use BioMAJ providing biomaj-cli.

Proper citation: CLI for BioMAJ (RRID:SCR_023980) Copy   

•   Source: SciCrunch Registry

https://github.com/GATB/bcalm

Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution.

Proper citation: BCALM 2 (RRID:SCR_023975) Copy   

•   Source: SciCrunch Registry

https://github.com/gpertea/gclib

Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time.

Proper citation: GCLib (RRID:SCR_024028) Copy   

•   Source: SciCrunch Registry

https://github.com/dutilh/CAT

Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies.

Proper citation: CAT and BAT (RRID:SCR_023988) Copy   

•   Source: SciCrunch Registry

https://github.com/RoelofBerg/limereg

Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image.

Proper citation: limereg (RRID:SCR_024097) Copy   

•   Source: SciCrunch Registry

https://neobio.sourceforge.net/

Software library of sequence alignment algorithms implemented in Java.

Proper citation: NeoBio (RRID:SCR_024131) Copy   

•   Source: SciCrunch Registry

http://murasaki.dna.bio.keio.ac.jp/wiki/

Software language-theory based homology detection tool across multiple large genomes.

Proper citation: Murasaki (RRID:SCR_024132) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/books/NBK179288/

Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats.

Proper citation: Entrez Direct (RRID:SCR_024136) Copy   

•   Source: SciCrunch Registry

https://doua.prabi.fr/software/njplot

Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

Proper citation: NJplot (RRID:SCR_024137) Copy   

•   Source: SciCrunch Registry

https://github.com/xdf-modules/libxdf

Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications.

Proper citation: Libxdf (RRID:SCR_024096) Copy   

•   Source: SciCrunch Registry

https://robokop.renci.org/

ROBOKOP system consists of web based user interface, API server, and several worker servers. Biomedical knowledge graph that integrates and semantically harmonizes important knowledge sources. Contains nodes representing entities such as genes, chemicals, and diseases, and edges representing relationships between them. Abstraction layer and user interface for knowledge graphs to support question answering. Used for reasoning over structured biomedical knowledge databases as part of NCATS translator and reasoner programs. ROBOKOP Knowledge Graph Builder constructs KG and provides extensible framework to handle graph query over and integration of federated data sources.

Proper citation: ROBOKOP (RRID:SCR_023437) Copy   

•   Source: SciCrunch Registry

https://github.com/mroosmalen/nanosv

Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

Proper citation: NanoSV (RRID:SCR_024127) Copy   

•   Source: SciCrunch Registry