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https://mc-stan.org/bayesplot/

Software R package providing extensive library of plotting functions for use after fitting Bayesian models.Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow.

Proper citation: bayesplot (RRID:SCR_024588) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/sib-swiss/pftools3

Software suite of tools to build and search generalized profiles.

Proper citation: PfTools (RRID:SCR_024158) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/bxlab/bx-python

Software Python library and associated set of scripts for rapid implementation of genome scale analyses.

Proper citation: python-bx (RRID:SCR_024202) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/books/NBK179288/

Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats.

Proper citation: Entrez Direct (RRID:SCR_024136) Copy   

•   Source: SciCrunch Registry

https://doua.prabi.fr/software/njplot

Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

Proper citation: NJplot (RRID:SCR_024137) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/NanoPlot

Software package as plotting tool for long read sequencing data and alignments.

Proper citation: NanoPlot (RRID:SCR_024128) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/OBITools/

Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.

Proper citation: OBITools (RRID:SCR_024141) Copy   

•   Source: SciCrunch Registry

https://www.orthanc-server.com/

Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases.

Proper citation: Orthanc (RRID:SCR_024145) Copy   

•   Source: SciCrunch Registry

http://openigtlink.org/

Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback.

Proper citation: OpenIGTLink (RRID:SCR_024148) Copy   

•   Source: SciCrunch Registry

http://www.itmat.upenn.edu/cohsi.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Informatics core for the purpose of promoting clinical research by collecting data from the Penn Health System.

Proper citation: Penn Community Outreach Using Health System Informatics Core (RRID:SCR_000304) Copy   

•   Source: SciCrunch Registry

https://psignifit.sourceforge.net/

Software toolbox to fit psychometric functions and to test hypotheses about psychometric data.

Proper citation: psignifit (RRID:SCR_024196) Copy   

•   Source: SciCrunch Registry

http://metabarcoding.org/sumaclust

Software tool aims to cluster sequences in a way that is fast and exact at the same time.

Proper citation: sumaclust (RRID:SCR_024352) Copy   

•   Source: SciCrunch Registry

https://ice.synthego.com/#/

Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data.

Proper citation: Inference of CRISPR Edits (RRID:SCR_024508) 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/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

http://www.glycosciences.de/tools/sumo/

Service that searches carbohydrate structures for motifs commonly used for carbohydrate classification, like N- and O-glycan cores, Lewis antigens, etc. Note: Sumo is currently under construction. Motif searches are a frequently used tool in proteomics. For carbohydrate structures, there are also many motifs classified in the literature, e.g. the Lewis antigens or the diverse O-glycan core structures. Sumo is a tool to locate such motifs in a carbohydrate structure given in LINUCS or in IUPAC nomenclature., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: sumo (RRID:SCR_001572) Copy   

•   Source: SciCrunch Registry