| aria2 | 1.35.0 | aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink. | Mar 25, 2025 | GPL-2.0 |
| bwa-index | 0.0.1 | create indexes for BWA from a fasta file | Mar 25, 2025 | MIT |
| doubletdetection | 2.4 | Doublet detection in single-cell RNA-seq data. | Mar 25, 2025 | MIT |
| fastqc | 0.0.1 | Run FastQC on sequenced reads | Mar 25, 2025 | MIT |
| gatk-dict | 0.0.1 | create a dictionary file from a fasta file | Mar 25, 2025 | MIT |
| jupytext | 0.8.3 | Jupyter notebooks as Markdown documents, Julia, Python or R scripts | Mar 25, 2025 | MIT |
| multicore-tsne | 0.1_d4ff4aab | Parallel t-SNE implementation with Python and Torch wrappers. | Mar 25, 2025 | BSD-3-Clause |
| nextflow-fastqc | 0.0.1 | — | Mar 25, 2025 | — |
| nf-bwa-index | 0.0.1 | create indexes for BWA from a fasta file | Mar 25, 2025 | MIT |
| phenograph | 1.5.2_15a4f8ac | Subpopulation detection in high-dimensional single-cell data | Mar 25, 2025 | MIT |
| r-bioqc | 1.5.2 | BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance. | Mar 25, 2025 | GPL (>=3) |
| r-conflicted | 1.0.1 | R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use. | Mar 25, 2025 | GPL-3 |
| r-epic | 1.1 | Package implementing EPIC method to estimate the proportion of immune, stromal, endothelial and cancer or other cells from bulk gene expression data. It is based on reference gene expression profiles for the main non-malignant cell types and it predicts the proportion of these cells and of the remaining "other cells" (that are mostly cancer cells) for which no reference profile is given. | Mar 25, 2025 | file LICENSE |
| r-harmony | 0_89f1226 | — | Mar 25, 2025 | — |
| r-immunarch | 0.5.2 | — | Mar 25, 2025 | Apache-2.0 |
| r-immunedeconv | 1.1.0 | collection of methods for immune cell deconvolution of bulk RNA-seq samples. | Mar 25, 2025 | BSD_3_clause |
| r-labelled | 1.1.0 | Work with labelled data imported from 'SPSS' or 'Stata' with 'haven' or 'foreign'. | Mar 25, 2025 | GPL-3 |
| r-limsolve | 1.5.5.3 | Functions that (1) find the minimum/maximum of a linear or quadratic function: min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(a_i*x_i) subject to equality constraints Ex=f and/or inequality constraints Gx>=h, (2) sample an underdetermined- or overdetermined system Ex=f subject to Gx>=h, and if applicable Ax~=b, (3) solve a linear system Ax=B for the unknown x. It includes banded and tridiagonal linear systems. The package calls Fortran functions from 'LINPACK'. | Mar 25, 2025 | GPL2 | GPL-3 |
| r-mcpcounter | a79614e | Estimating tissue-infiltrating immune and other stromal subpopulations abundances using gene expression | Mar 25, 2025 | GPL-3 |
| r-modules | 0.9.10 | Create reusable code modules in R. An alternative package management system for R, similar to module systems in Python, Ruby or JavaScript. | Mar 25, 2025 | Apache 2.0 + file LICENSE |
| r-questionr | 0.6.3 | Set of functions to make the processing and analysis of surveys easier : interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions. | Mar 25, 2025 | GPL (>= 2) |
| r-rmdformats | 0.3.3 | HTML formats and templates for 'rmarkdown' documents, with some extra features such as automatic table of contents, lightboxed figures, dynamic crosstab helper. | Mar 25, 2025 | GPL (>= 2) |
| r-xcell | 1.12 | Tissues are a complex milieu consisting of numerous cell types. In cancer, understanding the cellular heterogeneity in the tumor microenvironment is an emerging field of research. Numerous methods have been published in recent years for the enumeration of cell subsets from tissue expression profiles. However, the available methods suffer from three major problems: inferring cell subset based on gene sets learned and verified from limited sources; displaying only partial portrayal of the full cellular heterogeneity; and insufficient validation in mixed tissues. The xCell package performs cell type enrichment analysis from gene expression data for 64 immune and stroma cell types. xCell is a gene signatures-based method learned from thousands of pure cell types from various sources. xCell applies a novel technique for reducing associations between closley related cell types. xCell signatures were validated using extensive in-silico simulations and also cytometry immunophenotyping, and were shown to outperform previous methods. xCell allows researchers to reliably portray the cellular heterogeneity landscape of tissue expression profiles. | Mar 25, 2025 | GPL-3 |
| rectangle-packer | 1.1.0 | Pack a set of rectangles into an enclosing rectangle with minimum area | Mar 25, 2025 | MIT |
| reportsrender | 0.3.1 | Consistently render Rmarkdown documents and jupyter notebooks to HTML | Mar 25, 2025 | MIT |
