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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
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://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
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
Software tool for phylogenomic inference.
Proper citation: IQ TREE (RRID:SCR_021163) Copy
Software tool as next generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.Enables researchers to start analysis with raw DNA sequence data and finish with publication quality figures and statistical results. Used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities.
Proper citation: QIIME2 (RRID:SCR_021258) Copy
https://bitbucket.org/genomicepidemiology/kma/src/master/
Software mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.Used for aligning high quality reads against highly redundant databases, where unique matches often does not exist. Works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on users demands.
Proper citation: KMA (RRID:SCR_024054) Copy
Software parallel local alignment search tool for database comparison. NGS sequence similarity search tool providing significant accelerations of seeds based heuristic comparison methods.
Proper citation: PLAST (RRID:SCR_024170) Copy
https://github.com/ahmedmoustafa/JAligner
Open source software Java implementation of the Needleman�Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model.
Proper citation: JAligner (RRID:SCR_024050) Copy
https://seqan.github.io/lambda/
Software tool as local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools.
Proper citation: Lambda (RRID:SCR_024052) Copy
https://github.com/cboursnell/crb-blast
Software tool for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.
Proper citation: crb-blast (RRID:SCR_024325) Copy
https://www.tau.ac.il/~itaymay/cp/rate4site.html
Software tool for detecting conserved amino-acid sites by computing relative evolutionary rate for each site in multiple sequence alignment. Used for identification of functional regions in proteins.
Proper citation: Rate4Site (RRID:SCR_024222) Copy
Software for alignment free sequence comparison. Uses pattern of care and don't care positions. Compares frequencies of spaced words according to pre-defined pattern.
Proper citation: spaced (RRID:SCR_024345) Copy
Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic.
Proper citation: Logol (RRID:SCR_024104) Copy
https://www.sofa-framework.org/
Open source software framework targeting at real-time simulation, with emphasis on medical simulation.
Proper citation: sofa-apps (RRID:SCR_024346) Copy
https://gitlab.com/rki_bioinformatics/purple
Software tool for selecting target specific peptide candidates directly from given proteome sequence data.
Proper citation: purple (RRID:SCR_024183) Copy
http://bioinf.spbau.ru/sibelia
Software comparative genomics tool to assist biologists in analysing genomic variations that correlate with pathogens, or genomic changes that help microorganisms adapt in different environments. Used for evolutionary and genome rearrangement studies for multiple strains of microorganisms.
Proper citation: sibelia (RRID:SCR_024336) Copy
https://sibsim4.sourceforge.net/
Software tool designed to align expressed DNA sequence with genomic sequence, allowing for introns.
Proper citation: sibsim4 (RRID:SCR_024338) Copy
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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