imperial-college-research-computing
by imperial-college-research-computing (Organization)
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| Name | Latest Version | Summary | Updated | License |
|---|
| ragoo | 1.1 | RaGOO: fast and accurate reference-guided scaffolding of draft genomes | Mar 25, 2025 | MIT |
| pyipopt | 0.1 | — | Mar 25, 2025 | — |
| proovread | 2.14.0 | — | Mar 25, 2025 | — |
| ohana | 0.1 | Ohana is a suite of software for analyzing population structure and admixture history using unsupervised learning methods. We construct statistical models to infer individual clustering from which we identify outliers for selection analyses. This project is directed by Dr. Rasmus Nielsen at University of California Berkeley. Jade Cheng is funded by the Bioinformatics, Computer Science Department at Aarhus University and the Natural History Museum of Denmark at Copenhagen University. | Mar 25, 2025 | — |
| ants | 2.3.1 | Advanced Normalization Tools - ANTs extracts information from complex datasets that include imaging (Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit. | Mar 25, 2025 | BSD License |
| danpos | 2.2.2 | — | Mar 25, 2025 | — |
| svdetect | 0.7m | — | Mar 25, 2025 | GPL2,GPL3 |
| biogeme | 2.6a | Biogeme is an open source freeware designed for the maximum likelihood estimation of parametric models in general, with a special emphasis on discrete choice models. Two versions of the software are avaible. | Mar 25, 2025 | NONE |
| r-rcdd | 1.5 | R interface to (some of) cddlib (<https://github.com/cddlib/cddlib>). Converts back and forth between two representations of a convex polytope: as solution of a set of linear equalities and inequalities and as convex hull of set of points and rays. Also does linear programming and redundant generator elimination (for example, convex hull in n dimensions). All functions can use exact infinite-precision rational arithmetic. | Mar 25, 2025 | GPL-2 |
| r-lymphclon | 1.3.0 | A clonality score estimator that takes full advantage of the multi-biological-replicate structure of modern sequencing experiments; it specifically takes into account the reality that, typically, the clonal coverage is well below 0.1%. | Mar 25, 2025 | LGPL-2 |
| python-bioformats | 1.3.0 | Read and write life sciences file formats | Mar 25, 2025 | GNU General Public License v2 (GPLv2) |
| parcels | 0.9 | — | Mar 25, 2025 | MIT |
| gzstream | 1.5 | — | Mar 25, 2025 | LGPL |
| r-sgpls | 1.7 | Regularized version of partial least square approaches providing sparse, group, and sparse group versions of partial least square regression models (Liquet, B., Lafaye de Micheaux, P., Hejblum B., Thiebaut, R. (2016). | Mar 25, 2025 | GPL2,GPL3 |
| glib | 2.53.6 | Provides core application building blocks for libraries and applications written in C. | Mar 25, 2025 | LGPL-2.1 |
| cellprofiler | 2.2.0 | An open-source application for measuring phenotypes | Mar 25, 2025 | The BSD 3-Clause License |
| crest | 1.0 | CREST (Clipping Reveals Structure) is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data | Mar 25, 2025 | GPL-3 |
| r-hitandrun | 0.5_5 | The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints. | Mar 25, 2025 | GPL-3 |
| pyxnat | 1.0.1.0 | Xnat in Python | Mar 25, 2025 | BSD |
| boost-cpp | 1.64.0 | Free peer-reviewed portable C++ source libraries. | Mar 25, 2025 | Boost-1.0 |
| r-hypervolume | 3.0.2 | Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling. | Mar 25, 2025 | GPL-3 |
| prokaryote | 2.3.0 | UNKNOWN | Mar 25, 2025 | BSD License |
| bracer | 0.1 | BraCeR - reconstruction of B cell receptor sequences from single-cell RNA-seq data. | Mar 25, 2025 | Apache License 2.0 |
| changeo | 0.3.12 | Change-O is a collection of tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin (Ig) sequences, and reconstructing germline sequences. | Mar 25, 2025 | Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) |
| quip | 20170421 | — | Mar 25, 2025 | — |