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https://cran.r-project.org/package=wavethresh
Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.
Proper citation: wavethresh (RRID:SCR_024311) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A database of proteolytic pathways. Its goal is to contribute to the scientific community and the understanding of proteolysis by providing better tools and data to researchers and medical researchers.
Proper citation: PMAP (RRID:SCR_000740) Copy
https://wiki.nci.nih.gov/display/cageneindex/Cancer+Gene+Index+End+User+Documentation
THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data.
Proper citation: Cancer Gene Index (RRID:SCR_001117) Copy
http://web.bioinformatics.ic.ac.uk/eqtlexplorer/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics.
Proper citation: eQTL Visualization Tool (RRID:SCR_013413) Copy
http://pubchem.ncbi.nlm.nih.gov/
Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI).
Proper citation: PubChem (RRID:SCR_004284) Copy
Repository for all data, figures, theses, publications, posters, presentations, filesets, videos, datasets, negative data in a citable, shareable and discoverable manner with Digital Object Identifiers. Allows to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated in a way that the current scholarly publishing model does not allow. Features integration with ORCID, Symplectic Elements, can import items from Github and is a source tracked by Altmetric.com. Figshare gives users unlimited public space and 1GB of private storage space for free. Data are digitally preserved by CLOCKSS. Supported by Digital Science, a division of Macmillan Publishers Limited, as a community-based, open science project that retains its autonomy.
Proper citation: FigShare (RRID:SCR_004328) Copy
EuPathDB integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as database but unifies access to three major existing individual organism databases, PlasmoDB.org, ToxoDB.org and CryptoDB.org, and integrates these databases with data available from additional sources. Through ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases. EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with eukaryotic pathogens.
Proper citation: Eukaryotic Pathogen Database Resources (RRID:SCR_004512) Copy
Intergovernmental organisation funded by public research money from its member states in Europe. Groups and laboratories perform basic research in molecular biology and molecular medicine, training for scientists, students and visitors. Provides development of services, new instruments and methods, data and technology in its member states.
Proper citation: European Molecular Biology Laboratory (RRID:SCR_004473) Copy
https://www.fieldtriptoolbox.org
Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.
Proper citation: FieldTrip (RRID:SCR_004849) Copy
http://blast.ncbi.nlm.nih.gov/Blast.cgi
Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences.
Proper citation: NCBI BLAST (RRID:SCR_004870) Copy
https://bioconductor.org/packages/release/bioc/html/riboSeqR.html
Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.
Proper citation: riboSeqR (RRID:SCR_016947) Copy
https://bioconductor.org/packages/release/bioc/html/Rsubread.html
Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.
Proper citation: Rsubread (RRID:SCR_016945) Copy
https://bioconductor.org/packages/release/bioc/html/scran.html
Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection.
Proper citation: scran (RRID:SCR_016944) Copy
Software package for image acquisition, analysis, display, and archiving. Used to quantify the autoradiography data from Cyclone apparatus from Perkin Elmer.
Proper citation: OptiQuant Software (RRID:SCR_016769) Copy
Software R package of multivariate methods for the exploration and integration of biological datasets with a focus on variable selection. Used to analyse data from high throughput sequencing technologies and spectral imaging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: mixOmics (RRID:SCR_016889) 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://uk.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image
Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform.
Proper citation: Tools for NIfTI and ANALYZE image (RRID:SCR_016895) 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/gelles-brandeis/CoSMoS_Analysis
Software tools for analyzing co-localization single-molecule spectroscopy image data.
Proper citation: CoSMoS_Analysis (RRID:SCR_016896) Copy
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