| 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 |
| batchglm | 0.7.4 | Fast and scalable fitting of over-determined generalized-linear models (GLMs) | Mar 25, 2025 | BSD-3 |
| pyro-ppl | 1.3.1 | A Python library for probabilistic modeling and inference | Mar 25, 2025 | Apache 2.0 |
| cget | 0.1.8 | Cmake package retrieval | Mar 25, 2025 | boost |
| r-twosamplemr | 0.4.21 | Two Sample MR functions and interface to MR Base database. | Mar 25, 2025 | MIT |
| 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 |
| diffxpy | 0.7.4 | Fast and scalable differential expression analysis on single-cell RNA-seq data | Mar 25, 2025 | BSD-3 |
| r-proxysnps | 0.0.2 | Get proxy SNPs for a SNP in the 1000 Genomes Project. | Mar 25, 2025 | MIT |
| phenograph | 1.1.14 | Subpopulation detection in high-dimensional single-cell data | Mar 25, 2025 | MIT |
| 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-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 |
| r-quantpsyc | 1.5 | Contains functions useful for data screening, testing moderation, mediation and estimating power. | 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-harmony | 1.0 | Scalable integration of single cell RNAseq data for batch correction and meta analysis. | Mar 25, 2025 | MIT |
| 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-dirichletreg | 0.7_0 | Implements Dirichlet regression models in R. | 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-ff | 2.2_14 | The ff package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section (pagesize) in main memory - the effective virtual memory consumption per ff object. ff supports R's standard atomic data types 'double', 'logical', 'raw' and 'integer' and non-standard atomic types boolean (1 bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned), single (4 byte float with NAs). For example 'quad' allows efficient storage of genomic data as an 'A','T','G','C' factor. The unsigned types support 'circular' arithmetic. There is also support for close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and custom close-to-atomic types. ff not only has native C-support for vectors, matrices and arrays with flexible dimorder (major column-order, major row-order and generalizations for arrays). There is also a ffdf class not unlike data.frames and import/export filters for csv files. ff objects store raw data in binary flat files in native encoding, and complement this with metadata stored in R as physical and virtual attributes. ff objects have well-defined hybrid copying semantics, which gives rise to certain performance improvements through virtualization. ff objects can be stored and reopened across R sessions. ff files can be shared by multiple ff R objects (using different data en/de-coding schemes) in the same process or from multiple R processes to exploit parallelism. A wide choice of finalizer options allows to work with 'permanent' files as well as creating/removing 'temporary' ff files completely transparent to the user. On certain OS/Filesystem combinations, creating the ff files works without notable delay thanks to using sparse file allocation. Several access optimization techniques such as Hybrid Index Preprocessing and Virtualization are implemented to achieve good performance even with large datasets, for example virtual matrix transpose without touching a single byte on disk. Further, to reduce disk I/O, 'logicals' and non-standard data types get stored native and compact on binary flat files i.e. logicals take up exactly 2 bits to represent TRUE, FALSE and NA. Beyond basic access functions, the ff package also provides compatibility functions that facilitate writing code for ff and ram objects and support for batch processing on ff objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely with functionality from package 'bit': chunked looping, fast bit operations and coercions between different objects that can store subscript information ('bit', 'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows to work interactively with selections of large datasets and quickly modify selection criteria. Further high-performance enhancements can be made available upon request. | Mar 25, 2025 | GPL-2 | file LICENSE |
| naivede | 1.2.0 | The most trivial DE test based on likelihood ratio tests | 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 |
