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https://www.bioconductor.org/packages/release/bioc/html/ensembldb.html
Software R package to create and use Ensembl based annotation resources.
Proper citation: ensembldb (RRID:SCR_019103) Copy
https://gitlab.com/biomerieux-data-science/clustlasso
Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach.
Proper citation: clustLasso (RRID:SCR_018820) Copy
Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions.
Proper citation: PyRosetta (RRID:SCR_018541) Copy
Open source cross platform desktop geographic information system application that supports viewing, editing, and analysis of geospatial data. Functions as geographic information system software, allowing users to analyze and edit spatial information, in addition to composing and exporting graphical maps.
Proper citation: QGIS (RRID:SCR_018507) Copy
https://github.com/big-data-lab-team/spot
Open source software tool for file based localization of numerical perturbations in data analysis pipelines. Identifies components in pipeline, at resolution level of system process, that produce different results in different execution conditions.
Proper citation: Spot (RRID:SCR_018915) Copy
https://cran.r-project.org/web/packages/GALLO/vignettes/GALLO.html
Software R package developed for accurate annotation of genes and quantitative trait loci located in regions identified in common genomic analyses performed in livestock, such as Genome Wide Association Studies and transcriptomics using RNA-Sequencing. Allows graphical visualization of gene and QTL annotation results, data comparison among different grouping factors like methods, breeds, tissues, statistical models, studies and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens.
Proper citation: Genomic Annotation in Livestock for positional candidate LOci (RRID:SCR_019212) Copy
https://github.com/SMI/SmiServices
Software suite of tools for cataloguing and anonymising DICOM files, as used for Scottish Medical Imaging project. Software suite of microservices for loading, anonymising, linking and extracting large volumnes of dicom medical images to support medical research. Platform allows dicom tags extracted from clinical images to be loaded into MongoDB and relational database tables for purposes of generating anonymous linked research extracts including image anonymisation.
Proper citation: SMI Services (RRID:SCR_018881) Copy
https://cran.r-project.org/package=psych
Software R package for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis.Procedures for Psychological, Psychometric, and Personality Research. Used for personality, psychometric theory and experimental psychology.
Proper citation: psych (RRID:SCR_021744) Copy
https://github.com/AdmiralenOla/Scoary
Software tool that scores components of pan genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes.Designed to take gene presence absence.csv file from Roary as well as traits file created by user and calculate associations between all genes in accessory genome and traits. It reports list of genes sorted by strength of association per trait.
Proper citation: Scoary (RRID:SCR_021087) Copy
http://bioinformatics.org/biococoa/
Open source framework for bioinformatics written in Objective-C. Provides Cocoa and GNUstep programmers with full suite of APIs for handling and manipulating biological sequences.
Proper citation: BioCocoa (RRID:SCR_023977) Copy
http://biblatex-biber.sourceforge.net/
Software bibliography processing backend for LaTeX biblatex package. Supports unsurpassed feature set for automated conformance to complex bibliography style requirements such as labelling, sorting and name handling. BibTeX replacement for users of BibLaTeX.
Proper citation: Biber (RRID:SCR_023973) Copy
http://johnhommer.com/academic/code/aghermann
Sotware tool designed to run Process S simulations on Slow Wave Activity profiles from human EEG recordings.Produces set of sleep homeostat parameters which can be used to describe and differentiate individual sleepers, such as short vs long sleepers, early vs late, etc.Sleep research experiment manager, with facility for reading, displaying, and manual and semi-automatic scoring EEG recordings in edf format; conventional PSD and EEG Microcontinuity profiles; artifact detection; Independent Component Analysis; basic sleep analysis NREM-REM cycle detection.
Proper citation: Aghermann (RRID:SCR_023965) Copy
https://metacpan.org/dist/Bio-ASN1-EntrezGene
Software regular expression based Perl Parser for NCBI Entrez Gene genome databases. Parses ASN.1-formatted Entrez Gene record and returns data structure that contains all data items from gene record.
Proper citation: Bio-ASN1-EntrezGene (RRID:SCR_024056) Copy
https://metacpan.org/dist/AcePerl
Software provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously.
Proper citation: AcePerl (RRID:SCR_024057) Copy
https://odelaneau.github.io/shapeit4/
Software tool for estimation of haplotypes aka phasing for SNP array and high coverage sequencing data. The version 4 is refactored and improved version of SHAPEIT algorithm with multiple key additional features.
Proper citation: shapeit4 (RRID:SCR_024335) Copy
Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes.
Proper citation: CARD (RRID:SCR_023995) Copy
https://www.cs.cmu.edu/~ckingsf/software/sailfish/
Software tool that implements novel, alignment free algorithm for estimation of isoform abundances directly from set of reference sequences and RNA-seq reads.
Proper citation: sailfish (RRID:SCR_024326) Copy
https://github.com/fenderglass/Ragout/
Software tool for chromosome level scaffolding using multiple references. Given initial assembly fragments and one or multiple related references it produces chromosome scale assembly.
Proper citation: ragout (RRID:SCR_024206) Copy
https://metacpan.org/dist/Bio-SamTools
Software Perl interface to SamTools library for DNA sequencing.
Proper citation: Bio-SamTools (RRID:SCR_024066) Copy
Software de-novo sequence read assembler for microbial genomes.Designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.SKESA contigs could be connected into GFA graph using GFA connector.
Proper citation: skesa (RRID:SCR_024341) Copy
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