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https://bioconductor.org/packages/HTSFilter/

Software R package implements filtering procedure for replicated transcriptome sequencing data based on global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

Proper citation: htsfilter (RRID:SCR_024242) Copy   

•   Source: SciCrunch Registry

https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library

SIMD Smith-Waterman C/C++ library for use in genomic applications. SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages.

Proper citation: SSW Library (RRID:SCR_024089) Copy   

•   Source: SciCrunch Registry

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

Software R package to harmonize data management of multiple experimental assays performed on overlapping set of specimens.Provides user experience by extending concepts from SummarizedExperiment, supporting open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.

Proper citation: multiassayexperiment (RRID:SCR_024245) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-PrimerDesigner

Software package provides low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio-PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported.

Proper citation: Bio-PrimerDesigner (RRID:SCR_024082) Copy   

•   Source: SciCrunch Registry

https://svi-opensource.github.io/libics/

Software reference library for Image Cytometry Standard, an open standard for writing images of any dimensionality and data type to file, together with associated information regarding the recording equipment or recorded subject.Image Cytometry Standard file reading and writing.

Proper citation: libics (RRID:SCR_024085) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/groHMM/

Software R package for analysis of GRO-seq data. Used for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

Proper citation: groHMM (RRID:SCR_024237) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/genefilter/

Software R package provides some basic functions for filtering genes.

Proper citation: genefilter (RRID:SCR_024238) Copy   

•   Source: SciCrunch Registry

http://www.cprofiler.org/

Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output.

Proper citation: Composition Profiler (RRID:SCR_014630) Copy   

•   Source: SciCrunch Registry

http://www.cazy.org

Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site.

Proper citation: CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/ProP/

Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.

Proper citation: ProP Server (RRID:SCR_014936) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/psa/genewise/

Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool.

Proper citation: GeneWise (RRID:SCR_015054) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://posit.co/products/open-source/shinyserver/

Open Source platform to host multiple Shiny applications on single server.

Proper citation: shiny-server (RRID:SCR_024334) Copy   

•   Source: SciCrunch Registry

https://plast.inria.fr/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://spaced.gobics.de/

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   

•   Source: SciCrunch Registry

http://logol.genouest.org/

Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic.

Proper citation: Logol (RRID:SCR_024104) Copy   

•   Source: SciCrunch Registry