Tools   Select Another Resource Report Type

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

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   

•   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

https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revao_14dec2018

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://drawio-app.com/product/

Software tool as diagramming application that enables collaboration in real time.

Proper citation: draw.io (RRID:SCR_022939) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.thermofisher.com/de/de/home/digital-science/thermo-fisher-connect.html

Platform for connecting people, software, data, and equipment. Helps integrating software, instruments, and data across your lab’s existing ecosystem. Provides: workflows guide users through processes involving multiple systems;Centralized access to Thermo Fisher Scientific instrument service and expertise;Connectivity to monitor and maintain instruments and equipment;Granular data sharing controls to enhance collaboration;Secure environment.

Proper citation: ThermoFisher Connect Platform (RRID:SCR_023441) Copy   

•   Source: SciCrunch Registry

https://hla-net.eu/tools/

Software pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas. Tools for handling and analysing data with ambiquities.

Proper citation: Generate tools (RRID:SCR_023042) Copy   

•   Source: SciCrunch Registry

https://github.com/lambdaloop/anipose

Software package for 3D pose estimation. Uses DeepLabCut for 2D tracking and uses triangulation methods to project pose estimations into three dimensions.Toolkit for robust markerless 3D pose estimation.

Proper citation: Anipose (RRID:SCR_023041) Copy   

•   Source: SciCrunch Registry

https://github.com/jfarek/xatlas

Software tool as variant caller for SNVs and small indels. Implemented as software application written in C++ .

Proper citation: xAtlas (RRID:SCR_022987) Copy   

•   Source: SciCrunch Registry

https://www.starrlifesciences.com/product/small-animal-pulse-oximeter/

Software is part of MouseOx Plus pulse oximeter system.

Proper citation: Starr Life Sciences MouseOx Plus (RRID:SCR_022984) Copy   

•   Source: SciCrunch Registry