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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
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
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
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
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
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
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
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
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
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
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
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
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
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
https://github.com/MMTI/Toolkit_for_MIRA_LAB_Striatal_Segmentation
Software MATLAB pipeline that produces CNN-based segmentations of striatal regions of brain based on structural T1w image.
Proper citation: Toolkit for MIRA LAB Striatal Segmentation (RRID:SCR_023073) Copy
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
Software toolkit that enables real-time basecalling and several post-processing features that works on Oxford Nanopore Technologies sequencing platforms. Data processing toolkit that contains Oxford Nanopore Technologies basecalling algorithms, and several bioinformatic post-processing features. Provided as binaries to run on Windows, OS X and Linux platforms, as well as being integrated with MinKNOW, Oxford Nanopore device control software.
Proper citation: Guppy basecaller (RRID:SCR_023196) Copy
https://www.oracle.com/applications/crystalball/
Software spreadsheet based application for risk measurement and reporting, Monte Carlo simulation, time series forecasting, and optimization.Provides realistic and accessible way of modeling uncertainty, enabling you to measure and report on risk inherent in your key metrics.
Proper citation: Oracle Crystal Ball (RRID:SCR_023226) Copy
https://drawio-app.com/product/
Software tool as diagramming application that enables collaboration in real time.
Proper citation: draw.io (RRID:SCR_022939) Copy
https://github.com/sapporo-wes/sapporo-service
Software for standard implementation conforming to Global Alliance for Genomics and Health Workflow Execution Service API specification.
Proper citation: Sapporo service (RRID:SCR_023202) Copy
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