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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://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://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/helioalexandre/MouBeAT

Software package to analyze different behavioral tests in rodents semi-automatically. These tests include Open Field (OF), Elevated Plus Maze (EPM), Y-maze (YM) test and Morris Water Maze (MWM).

Proper citation: Mouse Behavioral Analysis Toolbox (RRID:SCR_023291) Copy   

•   Source: SciCrunch Registry

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

Software R package to read, write, manipulate and analyze variant call format data. Facilitates easy manipulation of variant call format (VCF) data.

Proper citation: vcfR (RRID:SCR_023453) Copy   

•   Source: SciCrunch Registry

https://grunwaldlab.github.io/poppr/

Software R package for analysis of populations with mixed modes of sexual and clonal reproduction. Used for genetic analysis of populations with mixed reproduction.

Proper citation: poppr (RRID:SCR_023452) Copy   

•   Source: SciCrunch Registry

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

Software R package to calculate various chance-corrected agreement coefficients among 2 or more raters. Among CAC coefficients covered are Cohen's kappa, Conger's kappa, Fleiss' kappa, Brennan-Prediger coefficient, Gwet's AC1/AC2 coefficients, and Krippendorff's alpha. Multiple sets of weights are proposed for computing weighted analyses.

Proper citation: Computing Chance Corrected Agreement Coefficients (RRID:SCR_023176) Copy   

•   Source: SciCrunch Registry

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

Software R package to calculate various intraclass correlation coefficients. Used to quantify inter-rater and intra-rater reliability.

Proper citation: Intraclass Correlations for Quantifying Inter Rater Reliability (RRID:SCR_023175) Copy   

•   Source: SciCrunch Registry

https://github.com/fritzsedlazeck/SURVIVOR

Software tool set for simulating and evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs. Used for for SV simulation, comparison and filtering.

Proper citation: SURVIVOR (RRID:SCR_022995) Copy   

•   Source: SciCrunch Registry

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

Software R package for analysis of paths from spatial tracking experiments such as Morris water maze and calculation of goal finding strategies. Used for in depth analysis of tracking coordinates from video.

Proper citation: Rtrack (RRID:SCR_023025) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/merqury

Software toolkit for reference free quality, completeness, and phasing assessment for genome assemblies. Genome assembly quality evaluation based on k-mers.

Proper citation: Merqury (RRID:SCR_022964) Copy   

•   Source: SciCrunch Registry