jdblischak
Recipes for packages in my channel are available at the GitHub repo linked above
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Packages
| Name | Latest Version | Summary | Updated | License |
|---|
| tiledbsoma-py | 1.10.2 | TileDB-SOMA Python API | Mar 25, 2025 | MIT |
| libtiledbsoma | 1.9.5 | TileDB-SOMA C++ library | Mar 25, 2025 | MIT |
| 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 |
| r-tiledbsoma | 1.10.2 | TileDB-SOMA R API | Mar 25, 2025 | MIT |
| tiledb | 2022_09_26 | TileDB sparse and dense multi-dimensional array data management | Mar 25, 2025 | MIT |
| r-workflowr | 0.11.0 | workflowr provides helper functions to get started using R Markdown to create a research website. | Mar 25, 2025 | MIT |
| r-dscrutils | 0.4.0 | Various R functions for interacting with and analyzing the results of a Dynamic Statistical Comparison (DSC) experiment. | Mar 25, 2025 | MIT |
| tiledb-py | 0.18.3.dev7.2022_11_15 | Python interface to the TileDB sparse and dense multi-dimensional array storage manager | Mar 25, 2025 | MIT |
| r-seqgendiff | 0.2.1 | Modifies/generates RNA-seq data for use in simulations. | Mar 25, 2025 | GPL-3 |
| sos-notebook | 0.19.1 | Script of Scripts (SoS): an interactive, cross-platform, and cross-language workflow system for reproducible data analysis | Mar 25, 2025 | BSD |
| 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 |
| r-ini | 0.3.0 | Parse simple '.ini' configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications. | Mar 25, 2025 | GPL-3 |
| 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-susier | 0.9.0 | The package implements a simple new way to perform variable selection in multiple regression ($y=Xb+e$), using computationally efficient variational Bayes approach. The methods implemented here are particularly well-suited to settings where some of the X variables are highly correlated, and the true effects are highly sparse (e.g. <20 non-zero effects in the vector $b$), although it is also useful to more general applications. | Mar 25, 2025 | MIT |
| 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) |
| 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 |
| r-tinier | 0.3.0 | Shrink image filesizes with the TinyPNG API <https://tinypng.com>. Works with .png and .jpg/.jpeg files, and can return the new image filepath to enable embedding in other image workflows/functions. | Jan 9, 2026 | MIT |
| 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 |
| 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-esabcv | 1.2.1 | These functions estimate the latent factors of a given matrix, no matter it is high-dimensional or not. It tries to first estimate the number of factors using bi-cross-validation and then estimate the latent factor matrix and the noise variances. For more information about the method, see Art B. Owen and Jingshu Wang 2015 archived article on factor model (http://arxiv.org/abs/1503.03515). | Mar 25, 2025 | GPL (>= 2) |
| 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-ggsci | 2.7 | A collection of 'ggplot2' color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows. | Mar 25, 2025 | GPL-3 | file LICENSE |
| 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-cowplot | 0.7.0 | Some helpful extensions and modifications to the 'ggplot2' package. In particular, this package makes it easy to combine multiple 'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc., as is often required for scientific publications. The package also provides a streamlined and clean theme that is used in the Wilke lab, hence the package name, which stands for Claus O. Wilke's plot package. | Mar 25, 2025 | GPL-2 |