Tools   Select Another Resource Report Type

http://www.nest-simulator.org/

Software tool as simulator for spiking neural network models that focuses on dynamics, size and structure of neural systems rather than on exact morphology of individual neurons. Used for any size spiking neurons networks including models of information processing, models of network activity dynamics, models of learning and plasticity.

Proper citation: NEST Simulator (RRID:SCR_002963) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/hclust/hclust.htm

Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HCLUST (RRID:SCR_009154) Copy   

•   Source: SciCrunch Registry

https://github.com/pybel

Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J.

Proper citation: PyBEL (RRID:SCR_017660) Copy   

•   Source: SciCrunch Registry

https://code.google.com/archive/p/kempbasu/

Software package implements two significance tests for comparing digital gene expression profiles. They provide two programs: Kemp for the frequentist test and Basu for the Bayesian test, and some auxiliary scripts.

Proper citation: kempbasu (RRID:SCR_024055) Copy   

•   Source: SciCrunch Registry

http://www.bioimagexd.net/

Software package for analyzing, processing and visualizing multi-dimensional microscopy images. Multipurpose postprocessing tool for bioimaging. Can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once.

Proper citation: BioImageXD (RRID:SCR_023979) Copy   

•   Source: SciCrunch Registry

http://www.bali-phy.org

Software application as simultaneous Bayesian inference of alignment and phylogeny. Used to estimate multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. to explore the joint space of alignment and phylogeny given molecular sequence data. BAli-Phy version 3 is model based co-estimation of alignment and phylogeny. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. Implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously.

Proper citation: BAli-Phy (RRID:SCR_023976) Copy   

•   Source: SciCrunch Registry

https://github.com/intake/intake

Software package for finding, investigating, loading and disseminating data.

Proper citation: Intake (RRID:SCR_024042) Copy   

•   Source: SciCrunch Registry

https://github.com/andersen-lab/ivar

Software package for viral amplicon based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.Contains intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.Following functions are implemented in iVar: trimming of primers and low-quality bases; consensus calling; variant calling both iSNVs and insertions/deletions; identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.

Proper citation: iVar (RRID:SCR_024045) Copy   

•   Source: SciCrunch Registry

https://changeo.readthedocs.io

Collection of software tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, and reconstructing germline sequences.

Proper citation: Change-O (RRID:SCR_023986) Copy   

•   Source: SciCrunch Registry

https://github.com/GATB/gatb-core

Software genome analysis toolbox with de-Bruijn graph. Library dedicated to genome assembly and analysis.

Proper citation: GATB (RRID:SCR_024024) Copy   

•   Source: SciCrunch Registry

https://github.com/gt1/bambamc

Software package contains lightweight C implementation of name collating BAM file input and BAM file output.

Proper citation: bambamc (RRID:SCR_023970) Copy   

•   Source: SciCrunch Registry

https://github.com/hall-lab/bamkit

Software tools for common BAM file manipulations.

Proper citation: bamkit (RRID:SCR_023969) Copy   

•   Source: SciCrunch Registry

https://github.com/jdidion/atropos

Software tool for specific, sensitive, and speedy trimming of NGS reads.

Proper citation: Atropos (RRID:SCR_023962) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/FAST

Software Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records.FAST workflows are designed for serial processing of flatfile biological sequence record databases per-sequence, rather than per-line, through UNIX pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FASTQ format is supported. FAST is designed for learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, and reproducibility. FAST tools expose the power of Perl and BioPerl to users in an easy-to-learn command-line paradigm.

Proper citation: FAST Analysis of Sequences Toolbox (RRID:SCR_024074) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-PrimerDesigner

Software package provides low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio-PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported.

Proper citation: Bio-PrimerDesigner (RRID:SCR_024082) Copy   

•   Source: SciCrunch Registry

http://rasmol.org/

Software package for molecular graphics visualisation.Used for visualisation of molecules.

Proper citation: rasmol (RRID:SCR_024208) Copy   

•   Source: SciCrunch Registry

http://www.bmsc.washington.edu/raster3d/raster3d.html

Software tools for generating high quality raster images of proteins or other molecules. Photorealistic molecular graphics. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing.

Proper citation: Raster3D (RRID:SCR_024220) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Biobase.html

Software R package provides functions that are needed by many other packages or which replace R functions. Base functions for Bioconductor.

Proper citation: Biobase (RRID:SCR_024224) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/fitbitScraper/index.html

Software R package to scrape data from Fitbit to generate graphs.

Proper citation: fitbitscraper (RRID:SCR_024273) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/fitdistrplus/index.html

Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data.

Proper citation: fitdistrplus (RRID:SCR_024274) Copy   

•   Source: SciCrunch Registry