Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://plexon.com/software-downloads/

Software tool used to control Plexon pattern generator for optogenetic stimulation.

Proper citation: Radiant (RRID:SCR_022645) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.freecad.org/

Open source parametric 3D modeler to design real life objects of any size. Parametric modeling allows modify your design by going back into your model history and changing its parameters.

Proper citation: FreeCAD (RRID:SCR_022535) Copy   

•   Source: SciCrunch Registry

https://github.com/kalininalab/d-StructMAn

Software tool provides annotation of non-synonymous single nucleotide variants in context of structural properties of resulting amino acid changes in corresponding proteins. Improved implementation of StructMAn, shipped in container form and extended to annotation of short in-frame indels and alterations arising as consequence of alternative splicing events. Produces range of structural features by combining information from experimentally resolved structures of many related proteins, which is unique feature of StructMAn family tools. Can also harness all protein structure models stored in AlphaFold Protein Structure Database.

Proper citation: d-StructMAn (RRID:SCR_022534) Copy   

•   Source: SciCrunch Registry

https://github.com/Hi5App

Software cross platform mobile application that supports 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, and distributed collaboration.

Proper citation: Hi5App (RRID:SCR_022819) Copy   

•   Source: SciCrunch Registry

https://github.com/replikation/What_the_Phage

Parallel multitool approach for phage prediction combined with annotation and classification downstream strategy. Used for identification and analysis of phage sequences. Phage identification via nextflow and docker or singularity.

Proper citation: What the Phage (RRID:SCR_022871) Copy   

•   Source: SciCrunch Registry

https://github.com/SydneyBioX/SurvBenchmark_package

Software package for comprehensive benchmarking study of survival analysis methods using both omics data and clinical data. Evaluates diverse collection of survival models for both clinical and omics datasets.

Proper citation: SurvBenchmark (RRID:SCR_022503) Copy   

•   Source: SciCrunch Registry