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http://www.acdlabs.com/resources/freeware/nmr_proc/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 27, 2016. A software package that provides 1D and 2D NMR tools as well as processing and interpretation for all other major analytical techniques (LC/MS, IR, Raman, and more) in one package. It also has support for structure verification and multiplet reports.

Proper citation: ACD/ NMR Processor (RRID:SCR_014679) Copy   

•   Source: SciCrunch Registry

https://github.com/pachterlab/kb_python

Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.).

Proper citation: kb_python (RRID:SCR_018213) Copy   

•   Source: SciCrunch Registry

http://treesoft.sourceforge.net/treebest.shtml

Software package to build, manipulate and display phylogenetic trees. Designed for building gene trees with known species tree and is highly efficient and accurate.

Proper citation: TreeBeST (RRID:SCR_018173) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/peppy/

Software python package for reading Portable Encapsulated Projects or PEPs in python.

Proper citation: peppy (RRID:SCR_021078) Copy   

•   Source: SciCrunch Registry

https://github.com/smajidian/phaseme

Software tool set to assess quality of per read phasing information and help to reduce errors during this process.

Proper citation: PhaseME (RRID:SCR_018739) Copy   

•   Source: SciCrunch Registry

https://www.biorxiv.org/content/10.1101/2020.09.24.311282v2.full

Software package to quickly transform microscope images into quality figures. User friendly tool for creating and formatting scientific figures, can export files into popular softwares like Adobe Illustrator, Microsoft Powerpoint, and Inkscape.

Proper citation: QuickFigures (RRID:SCR_019082) Copy   

•   Source: SciCrunch Registry

https://github.com/gatech-genemark/ProtHint

Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences.

Proper citation: ProtHint (RRID:SCR_021167) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/r8s/

Software package for estimating absolute rates of molecular evolution and divergence times on phylogenetic tree. Divergence time estimation on phylogenies.

Proper citation: r8s (RRID:SCR_021161) Copy   

•   Source: SciCrunch Registry

https://artistoo.net

Software toolbox, formerly called CPMjs, as framework to build interactive, explorable simulation models of cells and tissues in web browser. JavaScript library to build interactive Cellular Potts Models as command line applications or in web browser.

Proper citation: Artistoo (RRID:SCR_020983) Copy   

•   Source: SciCrunch Registry

https://docs.conda.io/en/latest/

Software tool as cross platform, language agnostic binary package manager. Open source package management system and environment management system that runs on Windows, macOS and Linux. Can quickly install, run, and update packages and their dependencies. Package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more. Created for Python programs, but it can package and distribute software for any language. Conda can be combined with continuous integration systems such as Travis CI and AppVeyor to provide frequent, automated testing of your code. Conda package and environment manager is included in all versions of Anaconda and Miniconda.

Proper citation: Conda (RRID:SCR_018317) Copy   

•   Source: SciCrunch Registry

https://github.com/benmarwick/cvequality

Software R package contains functions to test for significant differences in coefficients of variation among multiple groups of observations.

Proper citation: cvequality (RRID:SCR_019124) Copy   

•   Source: SciCrunch Registry

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

Software R package creating customizable presentation ready tables, summarizing data sets, regression models, and more. Used for publication ready data summary and analytic result tables.

Proper citation: gtsummary (RRID:SCR_021319) Copy   

•   Source: SciCrunch Registry

https://github.com/ikmb/gwas-qc/

Software tool as scalable GWAS Quality Control pipeline for biobank scale datasets.

Proper citation: GWAS Quality Control Pipeline (RRID:SCR_019241) Copy   

•   Source: SciCrunch Registry

https://estech.shinyapps.io/prisma_flowdiagram/

Software R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams. ShinyApp for producing PRISMA 2020 compliant flow diagrams.

Proper citation: PRISMA2020 (RRID:SCR_021053) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/plyranges/

Open source software R package for interacting with common Bioconductor classes Ranges and GenomicRanges. Grammar of genomic data transformation. Provides grammatical and consistent way of manipulating these classes to increase accessiblity for new Bioconductor users.

Proper citation: plyranges (RRID:SCR_021324) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ChIPseeker/

Software package to retrieve nearest genes around peak, annotate genomic region of peak, implements statstical methods for estimate significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare own dataset with those deposited in database.Several visualization functions are implemented to summarize coverage of peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Proper citation: ChIPseeker (RRID:SCR_021322) Copy   

•   Source: SciCrunch Registry

https://bioinf.shenwei.me/seqkit/

Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation.

Proper citation: SeqKit (RRID:SCR_018926) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=mHG

Software R package to run minimum hypergeometric test.

Proper citation: Minimum-Hypergeometric Test (RRID:SCR_018776) Copy   

•   Source: SciCrunch Registry

https://gbrs.readthedocs.io/en/latest/

Software suite of tools for reconstructing genomes using RNA-Seq data from multiparent population and for quantifying allele specific expression.

Proper citation: GBRS (RRID:SCR_020963) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=survival

Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

Proper citation: survival (RRID:SCR_021137) Copy   

•   Source: SciCrunch Registry