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https://psignifit.sourceforge.net/
Software toolbox to fit psychometric functions and to test hypotheses about psychometric data.
Proper citation: psignifit (RRID:SCR_024196) Copy
https://github.com/husonlab/jloda
Software Java library of data structures and algorithms.Provides some basic data structures and algorithms used by SplitsTree, Dendroscope and MEGAN.
Proper citation: JLODA (RRID:SCR_024076) Copy
https://gitlab.com/german.tischler/libmaus2
Software collection of data structures and algorithms. Contains I/O classes (single byte and UTF-8), bitio classes (input, output and various forms of bit level manipulation), text indexing classes (suffix and LCP array, fulltext and minute (FM), ...), BAM sequence alignment files input/output (simple and collating) and many lower level support classes.
Proper citation: libmaus2 (RRID:SCR_024077) Copy
https://bioconductor.org/packages/release/bioc/html/BridgeDbR.html
Software R pacakge provides functions and load identifier mapping databases in R. Uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.
Proper citation: bridgedbr (RRID:SCR_024231) Copy
https://bioconductor.org/packages/CNEr/
Software R package provides large scale identification and advanced visualization of sets of conserved noncoding elements.
Proper citation: CNEr (RRID:SCR_024233) Copy
https://bioconductor.org/packages/GenomeInfoDb/
Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order.
Proper citation: genomeinfodb (RRID:SCR_024235) Copy
https://bioconductor.org/packages/release/bioc/html/GenomicAlignments.html
Software R package provides efficient containers for storing and manipulating short genomic alignments. This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
Proper citation: genomicalignments (RRID:SCR_024236) Copy
https://bioconductor.org/packages/release/bioc/html/BiocGenerics.html
Software R package defines many S4 generic functions used in Bioconductor.
Proper citation: BiocGenerics (RRID:SCR_024226) Copy
https://github.com/vcflib/tabixpp
Software C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.Wrapper to tabix indexer
Proper citation: tabixpp (RRID:SCR_024107) Copy
https://bioconductor.org/packages/release/bioc/html/biomformat.html
Software R package for interfacing with BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, limited support for writing biom-object back to biom-format file.
Proper citation: biomformat (RRID:SCR_024228) Copy
https://bioconductor.org/packages/release/bioc/html/biovizBase.html
Software R package to provide set of utilities, color schemes and conventions for genomic data. Used for various high-level packages for biological data visualization.
Proper citation: biovizBase (RRID:SCR_024229) Copy
https://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html
Software library that exports C++ mmCIF accessors to Python.
Proper citation: Core Wrapper (RRID:SCR_024087) Copy
https://bioconductor.org/packages/release/data/annotation/html/GO.db.html
Software R package provides set of annotation maps describing entire Gene Ontology assembled using data from GO.
Proper citation: go.db (RRID:SCR_024241) Copy
https://bioconductor.org/packages/impute/
Software R package for imputation for microarray data.
Proper citation: impute (RRID:SCR_024243) Copy
https://bioconductor.org/packages/Mergeomics/
Software R pacakage for multidimensional data integration to identify pathogenic perturbations to biological systems. Used for integrating multidimensional omics disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. Includes Marker set enrichment analysis and Weighted Key Driver Analysis parts.
Proper citation: mergeomics (RRID:SCR_024244) Copy
https://github.com/wdecoster/nanolyse
Software package to remove reads mapping to the lambda phage genome from a fastq file.
Proper citation: NanoLyse (RRID:SCR_024125) Copy
https://bioconductor.org/packages/metagenomeSeq/
Software R package to determine features that are differentially abundant between two or more groups of multiple samples. Used to address the effects of both normalization and under-sampling of microbial communities on disease association detection and testing of feature correlations.
Proper citation: metagenomeseq (RRID:SCR_024246) Copy
https://github.com/mtholder/ncl
Software C++ class library for interpreting data files in NEXUS format. NEXUS Class Library software package is collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses.NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored.
Proper citation: libncl (RRID:SCR_024080) Copy
https://github.com/kdm9/libqes
Software C library with bioinformatic focus optimised for speed and clean API.
Proper citation: libqes (RRID:SCR_024083) Copy
https://github.com/toddy15/medicalterms
Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words.
Proper citation: medicalterms (RRID:SCR_024117) Copy
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