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http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
Proper citation: FastQC (RRID:SCR_014583) Copy
Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers.
Proper citation: GROMACS (RRID:SCR_014565) Copy
https://gemini.readthedocs.io/en/latest/
Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.
Proper citation: GEMINI (RRID:SCR_014819) Copy
Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information.
Proper citation: bio.tools (RRID:SCR_014695) Copy
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.
Proper citation: Bowtie 2 (RRID:SCR_016368) Copy
http://dgrapov.github.io/MetaMapR/
An open-source software program for integrating enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networks and display results using data visualization techniques.
Proper citation: MetaMapR (RRID:SCR_014685) Copy
http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html
Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots.
Proper citation: ConsensusClusterPlus (RRID:SCR_016954) Copy
http://bioconductor.org/packages/GenomicFeatures/
Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.
Proper citation: GenomicFeatures (RRID:SCR_016960) Copy
Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows.
Proper citation: BISE (RRID:SCR_016774) Copy
https://github.com/SofieVG/FlowSOM
Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise.
Proper citation: FlowSOM (RRID:SCR_016899) Copy
https://github.com/OpenSMFS/FRETBursts
Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data.
Proper citation: FRETBursts (RRID:SCR_016898) Copy
https://github.com/qiicr/dcmqi
Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.
Proper citation: dcmqi (RRID:SCR_016933) Copy
https://www.networkanalyst.ca/
Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data.
Proper citation: NetworkAnalyst (RRID:SCR_016909) Copy
http://prosightlite.northwestern.edu/
Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.
Proper citation: ProSight Lite (RRID:SCR_016908) Copy
Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.
Proper citation: MARRVEL (RRID:SCR_016871) Copy
https://github.com/PathwayAnalysisPlatform/PathwayMatcher
Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome.
Proper citation: PathwayMatcher (RRID:SCR_016759) Copy
https://pachterlab.github.io/sleuth/about
Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance.
Proper citation: sleuth (RRID:SCR_016883) Copy
http://www.bioconductor.org/packages/release/bioc/html/ropls.html
Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables.
Proper citation: ropls (RRID:SCR_016888) Copy
https://github.com/flo-compbio/xlmhg
Software Python package as a semiparametric test for enrichment in ranked lists. Used for determining gene set enrichment.
Proper citation: XL-mHG (RRID:SCR_016846) Copy
American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook.
Proper citation: Google (RRID:SCR_017097) Copy
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