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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/plger/scDblFinder
Software package for detection and handling of doublets/multiplets in single cell sequencing data.
Proper citation: scDblFinder (RRID:SCR_022700) Copy
https://github.com/PeterEckmann1/preprint-match
Software tool to match bioRxiv preprints with their corresponding PubMed paper.
Proper citation: PreprintMatch (RRID:SCR_022302) Copy
http://www.cgmartini.nl/index.php/downloads/tools/239-insane
Software tool for generating custom membranes for molecular simulations. Software Python script to setup Martini bilayer systems.
Proper citation: insane.py (RRID:SCR_022317) Copy
https://cran.r-project.org/web/packages/reshape2/index.html
Software R package to flexible rearrange, reshape and aggregate data. Reshape2 is reboot of reshape package.
Proper citation: reshape2 (RRID:SCR_022679) Copy
https://cran.r-project.org/web/packages/Peptides/index.html
Software R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
Proper citation: Peptides (RRID:SCR_022675) Copy
https://www.cbcb.umd.edu/software/epiviz
Software package as interactive visualization tool for functional genomics data. Interactive visual analytics for functional genomics data.
Proper citation: Epiviz (RRID:SCR_022796) Copy
https://CRAN.R-project.org/package=ggeffects
Software R package to create tidy data frames of marginal effects for ggplot from model outputs. Used to compute marginal effects and adjusted predictions from statistical models and returns result as tidy data frames.
Proper citation: ggeffects (RRID:SCR_022496) Copy
https://CRAN.R-project.org/package=betareg
Software R package for modeling beta distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of beta distributed response), bias corrected and bias reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided.
Proper citation: Betareg (RRID:SCR_022494) Copy
https://bioconductor.org/packages/monaLisa/
Software R package to work with sequence motifs in analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of obtained results are also provided.
Proper citation: monaLisa (RRID:SCR_022802) Copy
https://github.com/shooshtarilab/TMExplorer
Software package to improve studying tumour microenvironment with single cell sequencing. Developers may use this package to obtain data for validation of new algorithms and researchers interested in tumour microenvironment may use it to study specific cancers more closely. Curated collection of scRNAseq datasets sequenced from tumours.
Proper citation: TMExplorer (RRID:SCR_022768) Copy
https://spin.niddk.nih.gov/bax/software/TALOS-N/
Software package for prediction of protein backbone and sidechain torsion angles from NMR chemical shifts.
Proper citation: TALOS-N (RRID:SCR_022800) Copy
https://github.com/topepo/caret
Software R package that contains functions for training and plotting classification and regression models. Includes methods for pre-processing training data, calculating variable importance, and model visualizations.
Proper citation: Classification And Regression Training (RRID:SCR_022524) Copy
https://plexon.com/software-downloads/
Software tool used to control Plexon pattern generator for optogenetic stimulation.
Proper citation: Radiant (RRID:SCR_022645) Copy
https://CRAN.R-project.org/package=simplePHENOTYPES
Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy.
Proper citation: simplePHENOTYPES (RRID:SCR_022523) Copy
https://cran.r-project.org/web/packages/ranger/
Software R package as fast implementation of Random Forests for high dimentional data.
Proper citation: ranger (RRID:SCR_022521) Copy
https://bbknn.readthedocs.io/en/latest/
Software to identify each cell’s top neighbours in each batch separately instead of entire cell pool with no accounting for batch. Nearest neighbours for each batch are then merged to create final list of neighbours for cell. Aligns batches in a quick and lightweight manner.
Proper citation: BBKNN (RRID:SCR_022807) Copy
https://github.com/satijalab/sctransform
Software R package for normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.
Proper citation: sctransform (RRID:SCR_022146) Copy
https://gitlab.com/maaly7/emerald_metagenomics_annotations
Software metagenomics annotations pipeline that regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles in EuropePMC.
Proper citation: EMERALD METAGENOMICS ANNOTATIONS PIPELINE (RRID:SCR_022541) Copy
https://github.com/jkimlab/PLR-GEN
Software package for generation of pseudo long reads by using short reads of metagenomic sample and microbial reference genome sequences as input.
Proper citation: PLR-GEN (RRID:SCR_022264) Copy
https://stringr.tidyverse.org/
Software package to provide set of functions designed to make working with strings easy. Consistent wrappers for common string operations.
Proper citation: stringr (RRID:SCR_022813) Copy
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