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http://www.bioinformatics.babraham.ac.uk/projects/chipmonk/

Software tool to visualize and analyse ChIP-on-chip array data. Main features: * Import of data from Nimblegen arrays (other formats can be added if people send us examples) * Normalization of data (both per array and per probe) * Various data plotting options to assess data quality and the effectiveness of normalization * Creation of data groups for visualization and analysis * Visualization of data against an annotated genome. * Statistical analysis of data to find probes of interest * Creation of reports containing probes, data and genome annotation Note: This project is no longer being developed, but critical bug fixes will still be provided

Proper citation: ChIPMonk (RRID:SCR_002975) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/ms-lims/

Software that provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.

Proper citation: ms lims (RRID:SCR_002974) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View

An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results.

Proper citation: SMRT View (RRID:SCR_003029) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/pbh5tools

Software tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from cmp.h5 and bas.h5 files.

Proper citation: pbh5tools (RRID:SCR_003027) Copy   

•   Source: SciCrunch Registry

http://www.tongji.edu.cn/~zhanglab/DiNuP/

Software that compares the nucleosome profiles generated by high-throughput sequencing between different conditions. It provides a statistical p-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the FDR as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise.

Proper citation: DiNuP (RRID:SCR_003046) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/prorata/

A quantitative proteomics software program for accurate protein abundance ratio estimation with confidence interval evaluation.

Proper citation: ProRata (RRID:SCR_002988) Copy   

•   Source: SciCrunch Registry

http://www.bioperl.org

BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BioPerl (RRID:SCR_002989) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/gsea/

Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) Copy   

•   Source: SciCrunch Registry

http://r3cseq.genereg.net/Site/index.html

An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results.

Proper citation: r3Cseq (RRID:SCR_003198) Copy   

•   Source: SciCrunch Registry

http://creskolab.uoregon.edu/stacks/

A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

Proper citation: Stacks (RRID:SCR_003184) Copy   

•   Source: SciCrunch Registry

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.

Proper citation: RNAhybrid (RRID:SCR_003252) Copy   

•   Source: SciCrunch Registry

http://cal.tongji.edu.cn/PlantLoc/index.jsp

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif.

Proper citation: PlantLoc (RRID:SCR_003138) Copy   

•   Source: SciCrunch Registry

http://mrsfast.sourceforge.net/

A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)

Proper citation: mrsFAST (RRID:SCR_003128) Copy   

•   Source: SciCrunch Registry

http://acgt.cs.tau.ac.il/hyden/

Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request).

Proper citation: HYDEN (RRID:SCR_003126) Copy   

•   Source: SciCrunch Registry

http://genes.mit.edu/burgelab/miso/

Probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq and identifies differentially regulated isoforms or exons across samples.

Proper citation: MISO (RRID:SCR_003124) Copy   

•   Source: SciCrunch Registry

http://iimcb.genesilico.pl/MetaLocGramN/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice.

Proper citation: MetaLocGramN (RRID:SCR_003154) Copy   

•   Source: SciCrunch Registry

http://genecruiser.broadinstitute.org/genecruiser3/

A web service and web application for the annotation of microarray data providing integrated access to genomic information freely available from public data sources.

Proper citation: GeneCruiser (RRID:SCR_003153) Copy   

•   Source: SciCrunch Registry

http://www.psidev.info/

Initiative to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The main organizational unit is the work group, with a Gel Electrophoresis (GEL) work group, a Mass Spectrometry (MS) work group, a Molecular Interactions (MI) work group, a Protein Modifications (MOD) work group, a Proteomics Informatics (PI) work group, and a Sample Processing (SP) work group. The Gel Electrophoresis (GEL) work group aims to develop reporting requirements that supplement the Minimum Information About a Proteomics Experiment (MIAPE) parent document, describing the minimum information that should be reported about gel-based experimental techniques used in proteomics. The group will also develop data formats for capturing MIAPE-compliant data about gel electrophoresis and informatics performed on gel images. The Mass Spectrometry Standards Working Group defines community data formats and controlled vocabulary terms facilitating data exchange and archiving in the field of proteomics mass spectrometry. A past achievement is the mzData standard, which captures mass spectrometry output data. mzData's aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into a single format. mzData has been released but is now deprecated in favor of mzML. The Molecular Interactions workgroup is concentrating on improving the annotation and representation of molecular interaction data wherever it is published, be this in journal articles, authors web-sites or public domain databases; and improving the accessibility of molecular interaction data to the user community. By using a common standard data can be downloaded from multiple sources and easily combined using a single parser. The protein modification workgroup focuses on developing a consensus nomenclature and provide an ontology reconciling in a hierarchical representation the complementary descriptions of residue modifications. The protein modification ontology (PSI-MOD) is available in OBO format or in OBO.xml. A spreadsheet containing the mapping of the descriptive labels used in various databases and search engines, the consensus list of proposed short name for protein modifications established by collaborative effort of mass spectrometry community, and the proposed rules and recommendations for this nomenclature are available. These short names are included in the ontology as synonyms of the corresponding terms. The Proteomics Informatics Standards Group (PSI-PI) goals are to provide a set of minimal reporting requirements which augment the MIAPE reporting guidelines with respect to analysis of data derived from proteomics experiments; to provide vendor-neutral and standard formats for representing results of analyzing and processing experimental data; to foster adoption of the format by highlighting efforts made by vendors and individuals that utilize the format in their products. The remit of the Sample Processing Working Group is to produce reporting guidelines, data exchange formats and controlled vocabulary covering all separation techniques not considered to be "classical" one- or two-dimensional gel electrophoresis (cf. the Gel WG home page), along with other kinds of sample handling and processing (for example, "tagging" proteins or peptides, splitting, combining and storing samples). Where possible we seek to develop our products in collaboration with all proteomics stakeholders and, where relevant, developers from other standards communities, most notably metabolomics. * Minimum reporting requirements: The evolving Minimum Information About a Proteomics Experiment (MIAPE) documents offer guidelines on how to adequately report a proteomics experiment. It is expected that these documents will be published, and that the requirements within will be enforced by journals, compliant repositories and funders (cf. MIAME). * XML formats for data exchange: Derived from the FuGE general object model, the formats developed by this workgroup are designed to function both as standalone files and as part of a "parent" FuGE-ML document. These formats will facilitate data exchange between researchers, and submission to repositories or journals. * Controlled vocabularies (CVs) and ontology: Lists of clearly defined terms are crucial for the construction of unambiguously worded data files. In addition to providing supporting CVs for the individual data capture formats as part of the integrated PSI CV, the Sample Processing WG will contribute terms to the Functional Genomics Ontology (FuGO).

Proper citation: HUPO Proteomics Standards Initiative (RRID:SCR_003158) Copy   

•   Source: SciCrunch Registry

http://splicq.sourceforge.net/

A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data.

Proper citation: SpliCQ (RRID:SCR_003266) Copy   

•   Source: SciCrunch Registry

http://www.geospiza.com/

Developer of enterprise-class software systems for workflow management of genetic analysis. Geospiza has established itself as the life science industry's top software developer for meeting the combined laboratory, data management and analytical needs of biotechnology and pharmaceutical companies, universities, researchers, contract core and diagnostic laboratories involved in genetic testing and manufacturing bio-therapeutics. Geospiza's products are designed and built by biologists, enabling researchers to focus on the science, not the software. *GeneSifter Analysis Edition: Access easy-to-use statistical, visualization and annotation tools for Microarray and Next Generation Sequencing data. *GeneSifter Lab Edition: Manage cross-platform core lab operations from a single interface out-of-the-box.

Proper citation: Geospiza (RRID:SCR_003264) Copy   

•   Source: SciCrunch Registry