jdblischak
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| Name | Latest Version | Summary | Updated | License |
|---|
| bioconductor-flowclust | 3.12.2 | Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-scde | 1.99.1 | The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The scde package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures. The overall approach to the differential expression analysis is detailed in the following publication: "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi: 10.1038/nmeth.2967). The overall approach to subpopulation identification and characterization is detailed in the following pre-print: "Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F, Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734). | Mar 25, 2025 | custom |
| bioconductor-snplocs.hsapiens.dbsnp144.grch38 | 0.99.11 | SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-variancepartition | 1.4.2 | Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. | Mar 25, 2025 | GPL (>= 2) |
| bismark | 0.18.2_dev_a9c4148 | Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. | Mar 25, 2025 | GNU General Public License v3 (GPLv3) |
| cross-r-base | 4.2.0 | R is a free software environment for statistical computing and graphics. | Mar 25, 2025 | GPL-2.0-or-later |
| libtiledb-sql-py | 2.1.3 | libtiledb-sql-py is a Embedded Python SQL interface for TileDB arrays using the MyTile storage engine | Mar 25, 2025 | GPL-2.0-only |
| libtiledbsoma | 1.9.5 | TileDB-SOMA C++ library | Mar 25, 2025 | MIT |
| m2w64-htslib | 1.15.1 | C library for high-throughput sequencing data formats. | Mar 25, 2025 | MIT |
| r-adlift | 1.3_3 | Adaptive wavelet lifting transforms for signal denoising using optimal local neighbourhood regression, from Nunes et al. (2006) <doi:10.1007/s11222-006-6560-y>. | Mar 25, 2025 | GPL-2.0 and GPL-3.0 |
| r-archr | 1.0.2 | This package is designed to streamline scATAC analyses in R. | Mar 25, 2025 | GPL-2.0-or-later |
| r-ashr | 2.0.5 | The R package 'ashr' implements an Empirical Bayes approach for large-scale hypothesis testing and false discovery rate (FDR) estimation based on the methods proposed in M. Stephens, 2016, "False discovery rates: a new deal", <DOI:10.1093/biostatistics/kxw041>. These methods can be applied whenever two sets of summary statistics---estimated effects and standard errors---are available, just as 'qvalue' can be applied to previously computed p-values. Two main interfaces are provided: ash(), which is more user-friendly; and ash.workhorse(), which has more options and is geared toward advanced users. | Mar 25, 2025 | GPL (>= 3) |
| r-base | 4.2.0 | R is a free software environment for statistical computing and graphics. | Mar 25, 2025 | GPL-2.0-or-later |
| r-beeswarm | 0.2.3 | The bee swarm plot is a one-dimensional scatter plot like "stripchart", but with closely-packed, non-overlapping points. | Mar 25, 2025 | Artistic-2.0 |
| r-bfa | 0.4 | Provides model fitting for several Bayesian factor models including Gaussian, ordinal probit, mixed and semiparametric Gaussian copula factor models under a range of priors. | Mar 25, 2025 | GPL-3 |
| r-binhf | 1.0_1 | Binomial Haar-Fisz transforms for Gaussianization | Mar 25, 2025 | GPL (>= 2) |
| r-callr | 1.0.0 | It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that. | Mar 25, 2025 | MIT + file LICENSE |
| r-cate | 1.0.4 | Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing. | Mar 25, 2025 | GPL-2 |
| r-ccremover | 1.0.4 | Implements a method for identifying and removing the cell-cycle effect from scRNA-Seq data. The description of the method is in Barron M. and Li J. (2016) <doi | Mar 25, 2025 | GPL-3 |
| r-cellcycler | 0.1.6 | From gene expression data, filters out the sinusoidal genes and outputs relative times of the cells on the cell cycle. | Mar 25, 2025 | GPL (>= 2) |
| r-circular | 0.4_93 | Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific. | Mar 25, 2025 | GPL-2 |
| r-coga | 1.0.0 | Evaluation for density and distribution function of convolution of gamma distributions in R. Two related exact methods and one approximate method are implemented with efficient algorithm and C++ code. A quick guide for choosing correct method and usage of this package is given in package vignette. | Mar 25, 2025 | GPL (>= 3.0) |
| r-conicfit | 1.0.4 | Geometric circle fitting with Levenberg-Marquardt (a, b, R), Levenberg-Marquardt reduced (a, b), Landau, Spath and Chernov-Lesort. Algebraic circle fitting with Taubin, Kasa, Pratt and Fitzgibbon-Pilu-Fisher. Geometric ellipse fitting with ellipse LMG (geometric parameters) and conic LMA (algebraic parameters). Algebraic ellipse fitting with Fitzgibbon-Pilu-Fisher and Taubin. | Mar 25, 2025 | GPL (>= 3) |
| r-corshrink | 0.1_2 | Performs adaptive shrinkage of correlation and covariance matrices using a mixture model prior over the Fisher z-transformation of the correlations. A separate shrinkage intensity may be specifiedfor each cell of the correlation or the covariance table. | Mar 25, 2025 | GPL (>= 2) |
| r-covr | 2.2.2 | Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' (http://codecov.io) or 'Coveralls' (http://coveralls.io). Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code. | Mar 25, 2025 | MIT + file LICENSE |