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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://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   

•   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://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
  

http://statbio.github.io/Sargasso/

Software Python tool to disambiguate mixed species RNA-seq reads according to their species of origin.

Proper citation: Sargasso (RRID:SCR_023489) 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://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://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=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://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://atlasti.com/

Software qualitative analysis tool. Used by researchers and practitioners to uncover and systematically analyze complex phenomena hidden in unstructured data including text, multimedia, geospatial. Provides tools that let the user locate, code, and annotate findings in primary data material, to weigh and evaluate their importance, and to visualize relations between them. Consolidates documents and keeps track of all notes, annotations, codes and memos in all fields that require close study and analysis of primary material consisting of text, images, audio, video, and geo data. Provides analytical and visualization tools designed to open new interpretative views on material.

Proper citation: ATLAS.ti (RRID:SCR_022920) 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
  

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/ParkerLab/ataqv

Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments.

Proper citation: ataqv (RRID:SCR_023112) Copy   

•   Source: SciCrunch Registry