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https://github.com/replikation/What_the_Phage
Parallel multitool approach for phage prediction combined with annotation and classification downstream strategy. Used for identification and analysis of phage sequences. Phage identification via nextflow and docker or singularity.
Proper citation: What the Phage (RRID:SCR_022871) Copy
https://github.com/SydneyBioX/SurvBenchmark_package
Software package for comprehensive benchmarking study of survival analysis methods using both omics data and clinical data. Evaluates diverse collection of survival models for both clinical and omics datasets.
Proper citation: SurvBenchmark (RRID:SCR_022503) Copy
https://github.com/h2oai/h2o4gpu
Interface to H2O4GPU, collection of GPU solvers for machine learning algorithms.
Proper citation: h2o4gpu (RRID:SCR_022520) Copy
https://CRAN.R-project.org/package=shinythemes
Software R package Themes for use with Shiny.
Proper citation: shinythemes (RRID:SCR_022757) Copy
https://CRAN.R-project.org/package=shinyhelper
Software R package to add markdown helpfiles to shiny apps, using modal dialog boxes, with no need to observe each help button separately.
Proper citation: shinyhelper (RRID:SCR_022755) Copy
https://bids-matlab.readthedocs.io/en/latest/
Software MATLAB/Octave tools to interact with datasets conforming to Brain Imaging Data Structure format.
Proper citation: BIDS-Matlab (RRID:SCR_022292) Copy
https://CRAN.R-project.org/package=ggforce
Software R package providing missing functionality to ggplot2 through extension system introduced with ggplot2 v2.0.0.
Proper citation: ggforce (RRID:SCR_022575) Copy
https://github.com/ZhiGroup/IBD_benchmark
Software package as open source project benchmarks IBD detection tools with multiple measurements.
Proper citation: IBD Detection Tool Benchmark Tool (RRID:SCR_022850) Copy
http://cns.hkbu.edu.hk/RIDE.htm
Software Matlab based toolbox for temporal decomposition of EEG signal. Used for decomposition, reconstruction, and single trial analysis of event related potentials.
Proper citation: Residue Iteration Decomposition (RRID:SCR_022174) Copy
https://github.com/alexcwsmith/PiRATeMC
Software data management pipeline for camera synchronization and combined data directories.
Proper citation: Pi-based Remote Acquisition Technology for Motion Capture (RRID:SCR_022327) Copy
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
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
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
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
https://github.com/HChai01/ISGPRE
Software package for predicting interferon stimulated human genes.
Proper citation: ISGPRE (RRID:SCR_022730) Copy
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://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
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