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

Software R package as collection of functions to compute the Clopper-Pearson Confidence Interval and the required sample size. Density, distribution function, quantile function and random generation for the Generalized Binomial Distribution.Enhanced model for burn-in studies, where failures are tackled by countermeasures.

Proper citation: GenBiomApps (RRID:SCR_025542) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=km.ci

Software R package to compute various confidence intervals for the Kaplan-Meier estimator, namely: Peto's CI, Rothman CI, CI's based on Greenwood's variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by Nair and Hall and Wellner.

Proper citation: km.ci (RRID:SCR_025543) Copy   

•   Source: SciCrunch Registry

https://kimlab.io/brain-map/DevCCF/

Open access multimodal 3D atlases of developing mouse brain that can be used to integrate mouse brain imaging data for visualization, education, cell census mapping, and more. Atlas ages include E11.5, E13.5, E15.5, E18.5, P4, P14, and P56. Web platform can be utilized to visualize and explore the atlas in 3D. Downloadable atlas can be used to align multimodal mouse brain data. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system. Anatomical labels are manually drawn in 3D based on the prosomeric model. For additional references, the P56 template includes templates and annotations from the aligned Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) and aligned Molecular Atlas of the Adult Mouse Brain.

Proper citation: 3D Developmental Mouse Brain Common Coordinate Framework (RRID:SCR_025544) Copy   

•   Source: SciCrunch Registry

https://github.com/ratan-lab/sumo

Software for multiomic nonnegative matrix factorization.

Proper citation: Ratan-lab (SUMO) (RRID:SCR_025687) Copy   

•   Source: SciCrunch Registry

https://kimlab.io/brain-map/DevATLAS/

Whole brain developmental map of neuronal circuit maturation. Generated by whole brain spatiotemporal mapping of circuit maturation during early postnatal development. Standard reference for normative developmental trajectory of neuronal circuit maturation, as well as high throughput platform to pinpoint when and where circuit maturation is disrupted in mouse models of neurodevelopmental disorders, such as fragile X syndrome.

Proper citation: DevATLAS (RRID:SCR_025718) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/MetaCycle/vignettes/implementation.html

Software R package for detecting rhythmic signals from large scale time-series data. Used to evaluate periodicity in large scale data.

Proper citation: MetaCycle (RRID:SCR_025729) Copy   

•   Source: SciCrunch Registry

https://github.com/kbolton-lab/ArCH

Software somatic variant calling pipeline designed to detect low variant allele fraction clonal hematopoiesjsonsis variants.

Proper citation: ArCH (RRID:SCR_025975) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/STdeconvolve.html

Software R package as unsupervised, reference-free approach to infer latent cell-type proportions and transcriptional profiles within multi-cellular spatially-resolved pixels from spatial transcriptomics datasets.

Proper citation: STdeconvolve (RRID:SCR_025977) Copy   

•   Source: SciCrunch Registry

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

Software R package provides functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.

Proper citation: pracma (RRID:SCR_026021) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/methylSig.html

Software R package as whole genome DNA methylation analysis pipeline. Used for testing differentially methylated cytosines or regions in whole-genome bisulfite sequencing or reduced representation bisulfite sequencing experiments. Several options exist for either site-specific or sliding window tests, and variance estimation.

Proper citation: MethylSig (RRID:SCR_025849) Copy   

•   Source: SciCrunch Registry

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

Software package for optimal matching in R. Distance based bipartite matching using minimum cost flow, oriented to matching of treatment and control groups in observational studies. Routines are provided to generate distances from generalised linear models (propensity score matching), formulas giving variables on which to limit matched distances, stratified or exact matching directives, or calipers, alone or in combination.

Proper citation: optmatch (RRID:SCR_026185) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/DropletUtils.html

Software R package provides number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.

Proper citation: DropletUtils (RRID:SCR_026136) Copy   

•   Source: SciCrunch Registry

http://ibs.biocuckoo.org/online.php

Software package called illustrator of biological sequences. Can be used for representing organization of either protein or nucleotide sequences. Multiple options are provided, and biological sequences can be manipulated, recolored or rescaled in user-defined mode. Final representational artwork can be directly exported into publication-quality figure. Used as illustrator for presentation and visualization of biological sequences. Standalone package was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available

Proper citation: Illustrator for Biological Sequences (RRID:SCR_026149) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/BayesSpace.html

Software R package for clustering and enhancing resolution of spatial gene expression experiments. Clusters low-dimensional representation of gene expression matrix, incorporating spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

Proper citation: BayesSpace (RRID:SCR_026309) Copy   

•   Source: SciCrunch Registry

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

Software R package as dissimilarity-based functions for ecological analysis. Used for analyzing ecological data.

Proper citation: ecodist (RRID:SCR_026509) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/data/annotation/html/hgu133plus2.db.html

Software R package for Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data assembled using data from public repositories.

Proper citation: hgu133plus2 (RRID:SCR_026448) Copy   

•   Source: SciCrunch Registry

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

Software R package for estimation of time-dependent ROC curve and area under time dependent ROC curve in the presence of censored data, with or without competing risks. Confidence intervals of AUCs and tests for comparing AUCs of two rival markers measured on the same subjects can be computed, using the iid-representation of the AUC estimator.

Proper citation: timeROC (RRID:SCR_026444) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=hdf5r

Software R package as data model, library and file format for storing and managing large amounts of data.

Proper citation: hdf5r (RRID:SCR_026447) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/gettext/

Software tools that provide framework to help other GNU packages produce multi-lingual messages.

Proper citation: gettext (RRID:SCR_026490) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/statannotations/

Software Python package to optionally compute statistical test and add statistical annotations on plots generated with seaborn. Used to add statistical significance or custom annotations on seaborn plots.

Proper citation: statannotations (RRID:SCR_026623) Copy   

•   Source: SciCrunch Registry