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https://biosyntax.org/

Software for syntax highlighting for computational biology.

Proper citation: bioSyntax (RRID:SCR_016207) 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

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

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://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://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://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://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://github.com/BIMSBbioinfo/pigx_rnaseq

Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables.

Proper citation: PiGx-RNAseq (RRID:SCR_024160) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/BSgenome/

Software R package provides infrastructure shared by all the Biostrings-based genome data packages.

Proper citation: bsgenome (RRID:SCR_024230) Copy   

•   Source: SciCrunch Registry

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

Software R package for export and import classification trees and clusters to other programs.

Proper citation: ctc (RRID:SCR_024232) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/geneplotter/

Software R package provides functions for plotting genomic data

Proper citation: geneplotter (RRID:SCR_024234) 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://bioconductor.org/packages/release/bioc/html/AnnotationHub.html

Software R package to provide a client for the Bioconductor AnnotationHub web resource. AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered.

Proper citation: AnnotationHub (RRID:SCR_024227) 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