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http://bioconductor.org/packages/2.12/bioc/html/seqbias.html
Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.
Proper citation: seqbias (RRID:SCR_006832) Copy
http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html
Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data.
Proper citation: NormqPCR (RRID:SCR_003388) Copy
Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics.
Proper citation: Xenbase (RRID:SCR_003280) Copy
https://bioconductor.org/packages/genomation/
Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters.
Proper citation: genomation (RRID:SCR_003435) Copy
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/
Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) Copy
A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.
Proper citation: GEPAT (RRID:SCR_003597) Copy
http://jexpress.bioinfo.no/site/
Gene expression analysis software using Java.
Proper citation: J-Express (RRID:SCR_003609) Copy
A free archive and distribution service for unpublished preprints in the life sciences allowing authors to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published. Once an article is published in a journal, bioRxiv will update the preprint with a link to the published version.
Proper citation: bioRxiv (RRID:SCR_003933) Copy
A free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows.
Proper citation: Git (RRID:SCR_003932) Copy
http://mendel.stanford.edu/sidowlab/downloads/quest/
A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments.
Proper citation: Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) Copy
http://www.brl.bcm.tmc.edu/pash/pashDownload.rhtml
Performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing.
Proper citation: Pash 3.0 (RRID:SCR_004078) Copy
http://epigraph.mpi-inf.mpg.de/WebGRAPH/
A software for genome and epigenome analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: EpiGRAPH (RRID:SCR_004326) Copy
https://bcbio-nextgen.readthedocs.org/en/latest/
A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.
Proper citation: bcbio-nextgen (RRID:SCR_004316) Copy
The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.
Proper citation: PDBe - Protein Data Bank in Europe (RRID:SCR_004312) Copy
http://discovery.hsci.harvard.edu/
An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket.
Proper citation: Stem Cell Discovery Engine (RRID:SCR_004453) Copy
http://www.sanger.ac.uk/resources/software/artemis/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.
Proper citation: Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) Copy
A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events.
Proper citation: Tree and reticulogram REConstruction (RRID:SCR_004497) Copy
https://github.com/alyssafrazee/derfinder
R package for differential expression analysis of RNA-seq data.
Proper citation: DER Finder (RRID:SCR_004250) Copy
Curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from variety of living organisms based on IUBMB-approved transporter classification (TC) system. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. TC system is analogous to Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. TCDB users may submit their own sequenced proteins and descriptions for inclusion into database. The software tools used are all freely available for download. These programs are used for analysis of Protein and DNA sequences. Programs require UNIX server to run.
Proper citation: Transporter Classification Database (RRID:SCR_004490) 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
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