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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Software to support biomedical image computing.
Proper citation: CTK (RRID:SCR_024002) 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://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
https://www.bioinformatics.org/~tryphon/populations/
Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions.
Proper citation: Populations (RRID:SCR_024175) Copy
https://github.com/khowe/quicktree/
Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments.
Proper citation: quicktree (RRID:SCR_024205) Copy
https://github.com/a-slide/pycoQC
Software application to compute metrics and generate interactive QC plots for Oxford Nanopore technologies sequencing data.
Proper citation: pycoqc (RRID:SCR_024185) Copy
https://docs.airr-community.org/en/latest/packages/airr-python/overview.html
Software airr reference library provides basic functions and classes for interacting with AIRR Community Data Representation Standards, including tools for read, write and validation.
Proper citation: python-airr (RRID:SCR_024187) Copy
https://bioconductor.org/packages/release/bioc/html/annotate.html
Software R package for using R enviroments for annotation.
Proper citation: annotate (RRID:SCR_024221) Copy
https://bioconductor.org/packages/release/bioc/html/affyio.html
Software R package as routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing CEL and CDF file formats.
Proper citation: affyio (RRID:SCR_024223) Copy
https://bioconductor.org/packages/release/bioc/html/altcdfenvs.html
Software R package contains convenience data structures and functions to handle cdfenvs.
Proper citation: altcdfenvs (RRID:SCR_024225) Copy
https://github.com/aschafu/PSSH2
Software tools for creating the sequence-to-structure alignment database PSSH2.
Proper citation: pssh2 (RRID:SCR_024181) Copy
https://pyepl.sourceforge.net/
Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses.
Proper citation: pyepl (RRID:SCR_024182) Copy
https://github.com/PacificBiosciences/pbcopper
Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications.
Proper citation: pbcopper (RRID:SCR_024152) Copy
https://harvest.readthedocs.io/en/latest/content/parsnp.html
Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
Proper citation: Parsnp (RRID:SCR_024153) Copy
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files.
Proper citation: PDB2PQR (RRID:SCR_024155) Copy
https://github.com/sib-swiss/pftools3
Software suite of tools to build and search generalized profiles.
Proper citation: PfTools (RRID:SCR_024158) Copy
https://jydu.github.io/physamp/
Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree.
Proper citation: PhySamp (RRID:SCR_024159) Copy
https://cran.r-project.org/web/packages/biwt/index.html
Software R package for compute multivariate location, scale, and correlation estimates based on Tukey's biweight M-estimator.
Proper citation: biwt (RRID:SCR_024271) Copy
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