| scanpy | 1.5.2.dev0 | Single-Cell Analysis in Python. Scales to >1M cells. | Mar 25, 2025 | BSD-3 |
| legacy-api-wrap | 1.2 | Legacy API wrapper. | Mar 25, 2025 | GNU General Public v3 or later (GPLv3+) |
| harmonypy | 0.0.4 | A data integration algorithm. | Mar 25, 2025 | GNU General Public v3 or later (GPLv3+) |
| pyro-api | 0.1.2 | Generic API for dispatch to Pyro backends. | Mar 25, 2025 | Apache Software |
| pyro-ppl | 1.3.1 | A Python library for probabilistic modeling and inference | Mar 25, 2025 | Apache 2.0 |
| batchglm | 0.7.4 | Fast and scalable fitting of over-determined generalized-linear models (GLMs) | Mar 25, 2025 | BSD-3 |
| cget | 0.1.8 | Cmake package retrieval | Mar 25, 2025 | boost |
| diffxpy | 0.7.4 | Fast and scalable differential expression analysis on single-cell RNA-seq data | Mar 25, 2025 | BSD-3 |
| cellbender | 0.1 | CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. | Mar 25, 2025 | BSD3 |
| r-twosamplemr | 0.4.21 | Two Sample MR functions and interface to MR Base database. | Mar 25, 2025 | MIT |
| r-proxysnps | 0.0.2 | Get proxy SNPs for a SNP in the 1000 Genomes Project. | Mar 25, 2025 | MIT |
| r-googleauthr | 0.7.0 | Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility. | Mar 25, 2025 | MIT + file LICENSE |
| phenograph | 1.1.14 | Subpopulation detection in high-dimensional single-cell data | Mar 25, 2025 | MIT |
| r-quantpsyc | 1.5 | Contains functions useful for data screening, testing moderation, mediation and estimating power. | Mar 25, 2025 | GPL (>= 2) |
| r-searchable | 0.3.3.1 | Provides functionality for searching / subsetting and slicing named objects using 'stringr/i'-style modifiers by case (in)sensitivity, regular expressions or fixed expressions; searches uses the standard '[' operator and allows specification of default search behavior to either the search target (named object) and/or the search pattern. | Mar 25, 2025 | GPL-2 |
| r-tableone | 0.12.0 | Creates 'Table 1', i.e., description of baseline patient characteristics, which is essential in every medical research. Supports both continuous and categorical variables, as well as p-values and standardized mean differences. Weighted data are supported via the 'survey' package. See 'github' for a screen cast. | Mar 25, 2025 | GPL-2 |
| r-meta | 4.9_1 | User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from 'RevMan 5'; - prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression (if R package 'metafor' is installed); - generalised linear mixed models (if R packages 'metafor', 'lme4', 'numDeriv', and 'BiasedUrn' are installed); - produce forest plot summarising several (subgroup) meta-analyses. | Mar 25, 2025 | GPL (>= 2) |
| r-optparse | 1.4.4 | A command line parser inspired by Python's 'optparse' library to be used with Rscript to write "#!" shebang scripts that accept short and long flag/options. | Mar 25, 2025 | GPL (>= 2) |
| r-cit | 2.2 | A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables. | Mar 25, 2025 | Artistic-2.0 |
| pheweb | 1.1.14 | A tool to build multi-phenotype GWAS browsers | Mar 25, 2025 | AGPLv3 |
| r-harmony | 1.0 | Scalable integration of single cell RNAseq data for batch correction and meta analysis. | Mar 25, 2025 | MIT |
| bioconductor-rnbeads | 1.10.8 | RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale. | Mar 25, 2025 | GPL-3 |
| glmpca | 0.1.0 | Generalized PCA for dimension reduction of non-normally distributed data | Mar 25, 2025 | GNU Lesser General Public v3 or later (LGPLv3+) |
| naivede | 1.2.0 | The most trivial DE test based on likelihood ratio tests | Mar 25, 2025 | MIT |
| r-dirichletreg | 0.7_0 | Implements Dirichlet regression models in R. | Mar 25, 2025 | GPL-2 |
