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https://jarvis-mocap.github.io/jarvis-docs/

Software markerless 3D motion capture toolbox. Used for capturing precise 3D motion.

Proper citation: Joint Acquisition, Recording and Voxel based Inference System (RRID:SCR_022723) Copy   

•   Source: SciCrunch Registry

https://github.com/Frederik-D-Weber/zmax_edf_merge_converter

Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format.

Proper citation: zmax_edf_merge_converter (RRID:SCR_022567) Copy   

•   Source: SciCrunch Registry

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

Software R package implementation of cumulative link models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit models.

Proper citation: ordinal (RRID:SCR_022856) Copy   

•   Source: SciCrunch Registry

https://github.com/ggruenhagen3/coselens

Software R package to detect gene level differential selection between two groups of samples.Used for calculation of excess of non synonymous mutations between two groups.

Proper citation: Coselens (RRID:SCR_022578) Copy   

•   Source: SciCrunch Registry

https://github.com/tlancian/bio_cs

Software package for implementing algorithms proposed in Lanciano et al. "Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data".

Proper citation: bio_contrast_subgraph (RRID:SCR_022853) Copy   

•   Source: SciCrunch Registry

https://github.com/HChai01/ISGPRE

Software package for predicting interferon stimulated human genes.

Proper citation: ISGPRE (RRID:SCR_022730) Copy   

•   Source: SciCrunch Registry

https://github.com/jokergoo/EnrichedHeatmap

Software R package for comprehensive visualization of genomic signal associations. Visualizes enrichment of genomic signals on specific target regions. Used to visualize e.g. how histone marks are enriched to specific sites.

Proper citation: EnrichedHeatmap (RRID:SCR_023082) Copy   

•   Source: SciCrunch Registry

https://github.com/plaisier-lab/sygnal

Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts.

Proper citation: SYGNAL (RRID:SCR_023080) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=NMF

Software R package for nonnegative matrix factorization. Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms.

Proper citation: Algorithms and Framework for Nonnegative Matrix Factorization (RRID:SCR_023124) Copy   

•   Source: SciCrunch Registry

https://yeatmanlab.github.io/pyAFQ/

Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry.

Proper citation: Automated Fiber Quantification in Python (RRID:SCR_023366) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/

Software tool to create mutational matrices for all types of somatic mutations. Used to generate mutational matrices for set of samples with associated mutational catalogues. Used for optimized exploration and visualization of mutational patterns for all types of small mutational events. In addition to extending classification of single base substitutions, provides support for classifying doublet base substitutions and small insertions and deletions.

Proper citation: SigProfilerMatrixGenerator (RRID:SCR_023122) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/rms/

Software R package as collection of functions that assist with streamline modeling. Works with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.

Proper citation: Regression Modeling Strategies (RRID:SCR_023242) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Maaslin2.html

SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features.

Proper citation: MaAsLin2 (RRID:SCR_023241) Copy   

•   Source: SciCrunch Registry

https://ndphillips.github.io/FFTrees/

Software package as decision algorithms for solving binary classification problems. Faster and more frugal because every node allows making decision. Apart from being faster and requiring less information, FFTs tend to be robust against overfitting, and are easy to interpret, use, and communicate.

Proper citation: FFTrees (RRID:SCR_023359) Copy   

•   Source: SciCrunch Registry

https://remm.bihealth.org

Software tool that scores positions in human genome in terms of their regulatory probability. Regulatory Mendelian Mutation score was created for relevance prediction of non-coding variations (SNVs and small InDels) in human genome (hg19) in terms of Mendelian diseases.

Proper citation: ReMM score (RRID:SCR_023095) Copy   

•   Source: SciCrunch Registry

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

Software package as eukaryotic non model annotation pipeline.Used for bringing functional annotation to non-model eukaryotic transcriptomes to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. Addresses fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates of protein-coding transcripts.

Proper citation: EnTAP (RRID:SCR_023010) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ATACseqQC/

Software R package for post alignment quality assessment of ATAC-seq data. Package also contains functions to preprocess aligned ATAC-seq data for subsequent peak calling.

Proper citation: ATACseqQC (RRID:SCR_023103) Copy   

•   Source: SciCrunch Registry

https://github.com/ENCODE-DCC/atac-seq-pipeline

Software pipeline to process ATAC-Seq data. Used for automated end-to-end quality control and processing of ATAC-seq and DNase-seq data.

Proper citation: ENCODE ATAC-seq pipeline (RRID:SCR_023100) Copy   

•   Source: SciCrunch Registry

https://support.10xgenomics.com/single-cell-dna/software/pipelines/latest/what-is-cell-ranger-dna

Software analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation, and compare heterogeneity among cells. Used in processing of single cell DNA sequencing performed on 10x Chromium platform.

Proper citation: 10x Genomics Cellranger DNA (RRID:SCR_023221) Copy   

•   Source: SciCrunch Registry

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

Software R package for calculating and drawing variable trees. Variable trees display information about nested subsets of data frame.

Proper citation: vtree (RRID:SCR_023458) Copy   

•   Source: SciCrunch Registry