Tools   Select Another Resource Report Type

http://www.biomart.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.

Proper citation: BioMart Project (RRID:SCR_002987) Copy   

•   Source: SciCrunch Registry

https://github.com/xavierdidelot/clonalorigin

Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.

Proper citation: ClonalOrigin (RRID:SCR_016061) Copy   

•   Source: SciCrunch Registry

https://sanger-pathogens.github.io/Roary/

Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.

Proper citation: Roary (RRID:SCR_018172) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/PhenStat.html

Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.

Proper citation: PhenStat (RRID:SCR_021317) Copy   

•   Source: SciCrunch Registry

https://github.com/alexlib/KymoButler-1

Software tool as deep learning software for automated kymograph analysis. Uses artificial intelligence to trace lines in kymograph and extract information about particle movement. Speeds up analysis of kymographs by between 50 and 250 times, and comparisons show that it is as reliable as manual analysis.

Proper citation: KymoButler (RRID:SCR_021717) Copy   

•   Source: SciCrunch Registry

https://shiny.cnsgenomics.com/mRnd/

Web tool for calculations for Mendelian Randomization. Power calculations for Mendelian Randomization. Used to calculate statistical power for Mendelian Randomization study, using Non Centrality Parameter based approach.

Proper citation: mRnd (RRID:SCR_022156) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM

Software tool for inference using permutation methods. Requires Matlab or Octave. Can be executed from inside either environment, or directly from the shell and can be called from scripts. For users who are familiar with statistics and willing to use experimental analysis tools.

Proper citation: PALM (RRID:SCR_017029) Copy   

•   Source: SciCrunch Registry

http://www.vasotracker.com

Open source and stand alone software for assessing vascular reactivity. Used in pressure myograph system.

Proper citation: VasoTracker (RRID:SCR_017233) Copy   

•   Source: SciCrunch Registry

http://www.ariesepigenomics.org.uk/

Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time.

Proper citation: Accessible Resource for Integrated Epigenomics Studies (RRID:SCR_017492) Copy   

•   Source: SciCrunch Registry

https://models.physiomeproject.org

Repository of mainly CellML models powered by collection of software tools and libraries with PMR2 software suite as core power. Third party integration suites are RICORDO, Virtuoso, BiVeS/BudHat, OpenCOR, CombineArchive Web, WebCAT, Morre/MaSyMoS.

Proper citation: Physiome Model Repository (RRID:SCR_017374) Copy   

•   Source: SciCrunch Registry

https://github.com/shanemomara/omaraneurolab/tree/master/NeuroChaT

Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.

Proper citation: NeuroChaT (RRID:SCR_018020) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/goldman-srv/pandit

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains: * the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0) * nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as "templates"; * protein sequence alignments restricted to the family members for which nucleotide sequences are available * inferred phylogenetic trees for each alignment The data in PANDIT and the dataset's development have been frozen owing to a lack of funding support. The existing data, version 17.0 corresponding to Pfam 17.0, remain stable and, we hope, useful. The entire database is also available for download as a flatfile from this website.

Proper citation: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees (RRID:SCR_003321) Copy   

•   Source: SciCrunch Registry

http://old.genedb.org/genedb/glossina/

As of 12th March 2009, GeneDB provides access to the transcriptome of the Tsetse fly Glossina morsitans morsitans, the biological vector of African trypanosomiases. The current data set includes: >>7,015 contigs comprised of ESTs from Trypanosoma brucei infected midgut tissue (Lehane et al, Genome Biol. 2003;4(10):R63) >>7,493 contigs comprised of ESTs from salivary gland tissue >>18,404 contigs comprised of EST pooled from a range of different tissue- and developmental stage-specific libraries: head (2,700 ESTs), midgut (21,662 ESTs), reproductive organs (3, 438 ESTs), salivary gland (27,426 ESTs), larvae (2,304 ESTs), pupae (2,304 ESTs), fatbody (20,257 ESTs) (Attardo et al, Insect Molecular Biology 2006, 15(4):411-424), male and female whole bodies (19,968 ESTs). These data include the midgut and salivary gland ESTs used in the library specific clustering for the contig sets listed above. Initial automated annotations of product descriptions were manually revised by participants in two community annotation jamborees held under the auspice of the International Glossina Genome Initiative (IGGI) with funding by TDR. A Glossina morsitans morsitans genome project is currently also underway. To date, 2.4M capillary shotgun reads have been produced and the initial assembly is available to download via the ftp server and for blast analysis.

Proper citation: GeneDB Gmorsitans (RRID:SCR_004310) Copy   

•   Source: SciCrunch Registry

https://github.com/linnarsson-lab/cytograph

Software multistage analysis pipeline which progressively discovers cell types or states while mitigating impact of technical artifacts.Used for single cell analysis.

Proper citation: Cytograph (RRID:SCR_023101) Copy   

•   Source: SciCrunch Registry

https://pavlovia.org/

Web application as repository and launch platform for Psychopy experiments and other open-source tools.

Proper citation: Pavlovia (RRID:SCR_023320) Copy   

•   Source: SciCrunch Registry

https://www.rappsilberlab.org/software/xisearch/

Software and algorithm for analyzing protein protein cross linking mass spectrometry data. Library of routines for peptide based mass spectrometry. Contains search engine for identification of crosslinked peptides.

Proper citation: xiSEARCH (RRID:SCR_018395) Copy   

•   Source: SciCrunch Registry

http://web.cbio.uct.ac.za/~darren/rdp.html

Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes.

Proper citation: Recombination Detection Program (RRID:SCR_018537) Copy   

•   Source: SciCrunch Registry

https://bioweb.pasteur.fr/packages/pack@[email protected]

Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more.

Proper citation: Tracer (RRID:SCR_019121) Copy   

•   Source: SciCrunch Registry

https://github.com/MetaCell/nwb-explorer

Web application and standalone application to read, visualize and explore content of NWB:N 2 files.Used to share neurophysiological data in Neurodata Without Borders format.

Proper citation: NWB Explorer (RRID:SCR_021151) Copy   

•   Source: SciCrunch Registry

https://spikeinterface.readthedocs.io

Software tool as unified framework for spike sorting. Python framework to unify preexisting spike sorting technologies into single codebase and to facilitate straightforward comparison and adoption of different approaches.Used to reproducibly run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs.

Proper citation: SpikeInterface (RRID:SCR_021150) Copy   

•   Source: SciCrunch Registry