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https://github.com/mbillingr/libgdf

Software library for processing of biomedical signals. Provides generic storage for biosignals, such as EEG, ECG, MEG. C++ implementation of GDF - " general dataformat for biosignals" version V2.20.

Proper citation: libGDF (RRID:SCR_024075) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.aquamaniac.de/rdm/projects/libchipcard

Software library for generic access to chipcard readers and cards

Proper citation: Libchipcard (RRID:SCR_024071) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/brentp/cyvcf2

Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis.

Proper citation: cyvcf2 (RRID:SCR_024000) Copy   

•   Source: SciCrunch Registry

http://www.commontk.org/

Software to support biomedical image computing.

Proper citation: CTK (RRID:SCR_024002) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/kdm9/libqes

Software C library with bioinformatic focus optimised for speed and clean API.

Proper citation: libqes (RRID:SCR_024083) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://pharos.nih.gov/

Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC).

Proper citation: Illuminating the Druggable Genome (RRID:SCR_016924) Copy   

•   Source: SciCrunch Registry

https://github.com/zitmen/thunderstorm

Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging.

Proper citation: Thunder STORM (RRID:SCR_016897) Copy   

•   Source: SciCrunch Registry

http://crispr.hzau.edu.cn/CRISPR/

Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment.

Proper citation: CRISPR-P (RRID:SCR_016941) Copy   

•   Source: SciCrunch Registry

https://github.com/Crick-CancerGenomics/ascat

Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data.

Proper citation: ascat (RRID:SCR_016868) Copy   

•   Source: SciCrunch Registry

https://blake.bcm.edu/emanwiki/EMAN2

Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography.

Proper citation: EMAN (RRID:SCR_016867) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html

Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

Proper citation: clusterProfiler (RRID:SCR_016884) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/quicknii/

Histological brain section series aligner to volumetric atlases. Software tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems. Part of the QUINT workflow.

Proper citation: QuickNII (RRID:SCR_016854) Copy   

•   Source: SciCrunch Registry

https://github.com/TGAC/KAT

Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies.

Proper citation: KAT (RRID:SCR_016741) Copy   

•   Source: SciCrunch Registry