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https://github.com/SouthGreenPlatform/metaXplor
Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures.
Proper citation: metaXplor (RRID:SCR_019025) Copy
https://github.com/LCSB-BioCore/GigaSOM.jl
Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets.
Proper citation: GigaSOM.jl (RRID:SCR_019020) Copy
http://crdd.osdd.net/raghava/vicmpred/index.html
Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule.
Proper citation: VICMpred (RRID:SCR_019039) Copy
http://pyntacle.css-mendel.it/
Software Python package and command line tool for graphs analysis. Used to search for important components of graphs. Implements and provides ancillary methods for community finding, set operations between graphs, and quick data type conversion tools.
Proper citation: Pyntacle (RRID:SCR_019030) Copy
https://bitbucket.org/berkeleylab/metabat/src/master/
Software statistical framework for reconstructing genomes from metagenome data. Open source software tool for accurately reconstructing single genomes from complex microbial communities.
Proper citation: MetaBAT (RRID:SCR_019134) Copy
https://github.com/constantAmateur/SoupX
Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data.
Proper citation: SoupX (RRID:SCR_019193) Copy
https://github.com/statOmics/tradeSeq
Software tool as suite of tests for identifying dynamic temporal gene regulation using single cell RNA-seq data.Trajectory based differential expression analysis for sequencing data.
Proper citation: tradeSeq (RRID:SCR_019238) Copy
http://bioinformatics.sdstate.edu/go/
Software graphical gene set enrichment tool for animals and plants. Graphical web application to gain insights from gene sets. Features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for retrieval of pathway diagrams and protein-protein interaction networks.
Proper citation: ShinyGO (RRID:SCR_019213) Copy
https://bioconductor.org/packages/biomaRt/
Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis.
Proper citation: biomaRt (RRID:SCR_019214) Copy
https://github.com/ShaokunAn/D-EE
Software tool for distributed dimensionality reduction and visualization. Distributed software for visualizing intrinsic structure of large scale single cell data written in C language. Its distributed storage and distributed computation technique allows efficiently analyze large scale single cell data at cost of constant time speedup.
Proper citation: D-EE (RRID:SCR_019058) Copy
https://bioconductor.org/packages/ReactomePA/
Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.
Proper citation: ReactomePA (RRID:SCR_019316) Copy
https://github.com/BNadel/GEDIT
Software tool for accurate cell type quantification from gene expression data. Uses gene expression data to estimate cell type abundances. Allows user to supply custom reference matrices.
Proper citation: GEDIT (RRID:SCR_019277) Copy
Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers.
Proper citation: ImJoy (RRID:SCR_020935) Copy
http://srna-workbench.cmp.uea.ac.uk
Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals.
Proper citation: UEA sRNA Workbench (RRID:SCR_020947) Copy
https://github.com/Pithikos/C-Thread-Pool
Software for minimal but powerful thread pool in ANSI C.
Proper citation: C Thread Pool (RRID:SCR_023999) Copy
https://github.com/smirarab/sepp/
Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem.
Proper citation: sepp (RRID:SCR_024327) Copy
https://www.teuniz.net/edflib/
Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files.
Proper citation: EDFlib (RRID:SCR_024010) Copy
http://www.dclunie.com/dicom3tools.html
Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files.
Proper citation: Dicom3tools (RRID:SCR_024008) Copy
https://github.com/stamatak/AxPcoords.dist
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets.
Proper citation: AxPcoords (RRID:SCR_023971) Copy
http://sco.h-its.org/exelixis/web/software/AxParafit/index.html
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets.
Proper citation: AxParafit (RRID:SCR_023968) Copy
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