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http://www.broadinstitute.org/igv/
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
Proper citation: Integrative Genomics Viewer (RRID:SCR_011793) Copy
http://i122server.vu-wien.ac.at/CANGS1.1/
A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.
Proper citation: CANGS (RRID:SCR_011837) Copy
https://github.com/hyattpd/Prodigal
Software tool for protein coding gene prediction for prokaryotic genomes.
Proper citation: Prodigal (RRID:SCR_011936) Copy
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
http://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html
Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.
Proper citation: ChIPpeakAnno (RRID:SCR_012828) Copy
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
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
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
Ratings or validation data are available for this resource
http://ccb.jhu.edu/software/tophat/index.shtml
Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.
Proper citation: TopHat (RRID:SCR_013035) Copy
A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure.
Proper citation: Jalview (RRID:SCR_006459) Copy
https://github.com/arq5x/bedtools2
A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
Proper citation: BEDTools (RRID:SCR_006646) Copy
Software to determine most stable reference (housekeeping) genes from set of tested candidate reference genes in given sample panel. From this, gene expression normalization factor can be calculated for each sample based geometric mean of user-defined number of reference genes.
Proper citation: geNORM (RRID:SCR_006763) Copy
http://www.bioconductor.org/packages/2.11/bioc/html/ShortRead.html
Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats.
Proper citation: ShortRead (RRID:SCR_006813) Copy
https://sedfitsedphat.nibib.nih.gov/software/default.aspx
Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.
Proper citation: SEDFIT (RRID:SCR_018365) Copy
https://github.com/blackrim/phyutility
Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI.
Proper citation: Phyutility (RRID:SCR_018545) Copy
http://www.prisma-statement.org/
Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.
Proper citation: PRISMA (RRID:SCR_018721) Copy
http://bioinf.wehi.edu.au/software/elda/
Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly.
Proper citation: ELDA (RRID:SCR_018933) Copy
https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/
Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR.
Proper citation: PROCHECK (RRID:SCR_019043) Copy
https://cran.r-project.org/web/packages/igraph/
Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus.
Proper citation: igraph (RRID:SCR_019225) Copy
Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system.
Proper citation: OpenClinica (RRID:SCR_019223) Copy
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