Tools   Select Another Resource Report Type

https://github.com/ylab-hi/ScanITD

Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation.

Proper citation: ScanITD (RRID:SCR_018886) Copy   

•   Source: SciCrunch Registry

https://github.com/davidebolo1993/TRiCoLOR

Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments.

Proper citation: TRiCoLOR (RRID:SCR_018801) Copy   

•   Source: SciCrunch Registry

https://beikolab.cs.dal.ca/software/STAMP

Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups.

Proper citation: STAMP (RRID:SCR_018887) Copy   

•   Source: SciCrunch Registry

http://tools.dice-database.org/GOnet/)

Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.

Proper citation: GOnet (RRID:SCR_018977) Copy   

•   Source: SciCrunch Registry

http://enterobase.warwick.ac.uk/

Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella.

Proper citation: EnteroBase (RRID:SCR_019019) Copy   

•   Source: SciCrunch Registry

http://dgenies.toulouse.inra.fr/

Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.

Proper citation: D-GENIES (RRID:SCR_018967) Copy   

•   Source: SciCrunch Registry

https://nanopore.usegalaxy.eu/

Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.

Proper citation: NanoGalaxy (RRID:SCR_018912) Copy   

•   Source: SciCrunch Registry

https://nrdg.github.io/fracridge

Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python.

Proper citation: fracridge (RRID:SCR_019045) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/DNAcopy.html

Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.

Proper citation: DNAcopy (RRID:SCR_012560) Copy   

•   Source: SciCrunch Registry

http://autodock.scripps.edu/

Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids.

Proper citation: AutoDock (RRID:SCR_012746) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/edgeR/

Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.

Proper citation: edgeR (RRID:SCR_012802) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/

A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.

Proper citation: IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) Copy   

•   Source: SciCrunch Registry

https://github.com/bedops/bedops

A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets.

Proper citation: BEDOPS (RRID:SCR_012865) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/featureCounts/

A read summarization program, which counts mapped reads for the genomic features such as genes and exons.

Proper citation: featureCounts (RRID:SCR_012919) Copy   

•   Source: SciCrunch Registry

http://bioinfo2.ugr.es/NGSmethDB/

A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes.

Proper citation: NGSmethDB (RRID:SCR_012847) Copy   

•   Source: SciCrunch Registry

http://mitobreak.portugene.com/cgi-bin/Mitobreak_home.cgi

Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.

Proper citation: MitoBreak (RRID:SCR_012949) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/DEXSeq.html

Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Proper citation: DEXSeq (RRID:SCR_012823) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/minfi.html

Software tools for analyzing and visualizing Illumina''s 450k array data.

Proper citation: minfi (RRID:SCR_012830) Copy   

•   Source: SciCrunch Registry

http://repeatmasker.org/

Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).

Proper citation: RepeatMasker (RRID:SCR_012954) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/affy.html

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

Proper citation: affy (RRID:SCR_012835) Copy   

•   Source: SciCrunch Registry