Tools   Select Another Resource Report Type

http://users.sussex.ac.uk/~lionelb/MVGC/

Matlab software toolkit designed to facilitate Granger-causal analysis with multivariate and possibly multi-trial time series data. Annotated demonstration scripts are available which may be used as templates to assist in this the toolbox's functions.

Proper citation: MVGC Multivariate Granger Causality Matlab Toolbox (RRID:SCR_015755) Copy   

•   Source: SciCrunch Registry

https://github.com/EpistasisLab/ReBATE

Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity .

Proper citation: ReBATE (RRID:SCR_017139) Copy   

•   Source: SciCrunch Registry

https://github.com/bionitio-team/bionitio

Open source software tool to provide template for command line bioinformatics tools in various programming languages. Program reads one or more input FASTA files, computes variety of statistics on each file, and prints tabulated output. Used as basis for learning and as foundation for starting new projects.

Proper citation: Bionitio (RRID:SCR_017259) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/Fastaq

Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together.

Proper citation: Fastaq (RRID:SCR_016091) Copy   

•   Source: SciCrunch Registry

http://fastqtl.sourceforge.net/

Software for mapping of molecular phenotypes that implements a new permutation scheme to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels in large-scale datasets. It is used to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq.

Proper citation: Fastqtl (RRID:SCR_016093) Copy   

•   Source: SciCrunch Registry

http://harvest.readthedocs.org/en/latest/content/harvest-tools.html

Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations.

Proper citation: Harvest-tools (RRID:SCR_016132) Copy   

•   Source: SciCrunch Registry

http://CRAN.R-project.org/package=RVAideMemoire

Software package that contains miscellaneous functions useful in biostatistics, such as univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions shorten existing procedures and implement plotting functions that can be used with a variety of methods and packages.

Proper citation: R package: RVAideMemoire (RRID:SCR_015657) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/CHROMELEON7

Software system to support chromatography operations, to ensure data quality and manage all the analytical processes from instrument control, to raw data storage and processing, through to generating the final results.

Proper citation: Chromeleon Chromatography Data System (CDS) Software (RRID:SCR_016874) Copy   

•   Source: SciCrunch Registry

https://github.com/lrq3000/spm_auto_reorient_coregister

Open source cross platform for automatic AC-PC realignment, reorientation and coregistration robust to brain damage in Statistical Parametric Mapping. Set of routines to perform auto reorient and auto coregistration in toolbox SPM12.

Proper citation: spm_auto_reorient_coregister (RRID:SCR_017281) Copy   

•   Source: SciCrunch Registry

https://github.com/QTIM-Lab/DeepNeuro

Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.

Proper citation: DeepNeuro (RRID:SCR_016911) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html

Software package which brings to R color scales. Created for the Python matplotlib library.

Proper citation: viridis (RRID:SCR_016696) 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://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://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://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://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