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HCC / packages

Package Name Access Summary Updated
phono3py public A simulation package of phonon-phonon interaction related properties 2023-06-16
circleator public Flexible circular visualization of genome-associated data with BioPerl and SVG. 2023-06-16
apache-batik public Batik is a Java-based toolkit for applications or applets that want to use images in the Scalable Vector Graphics (SVG) format for various purposes, such as display, generation or manipulation. 2023-06-16
gramdist public GramDist is a utility for generating dissimilarity matrices using the relative complexity measure, a computationally efficient and alignment free evolutionary distance metric. 2023-06-16
gramcluster public GramCluster is a fast and accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets. 2023-06-16
gramalign public GramAlign is a time-efficient progressive Multiple Sequence Alignment (MSA) algorithm. 2023-06-16
gradle public Gradle is an open-source build automation tool focused on flexibility and performance. 2023-06-16
gensim public Topic Modelling for Humans 2023-06-16
r-rhierbaps public rhierbaps is R implementation of hierBAPS. 2023-06-16
ncarg-rangs public RANGS is the abbreviation of 'Regionally Accessible Nested Global Shorelines'. 2023-06-16
bash-kernel public A bash kernel for Jupyter 2023-06-16
persim public Distances and representations of persistence diagrams 2023-06-16
sumo public Heavy weight plotting tools for ab initio solid-state calculations. 2023-06-16
matlab-kernel public Jupyter Kernel for Matlab 2023-06-16
python-ripser public A Lean Persistent Homology Library for Python 2023-06-16
cellranger public Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis. 2023-06-16
bcl2fastq2 public The Illumina bcl2fastq2 Conversion Software v2.20 demultiplexes sequencing data and converts base call (BCL) files into FASTQ files. 2023-06-16
libxslt public The XSLT C library developed for the GNOME project. 2023-06-16
libxml2 public The XML C parser and toolkit of Gnome. 2023-06-16
fbpca public Fast computations of PCA/SVD/eigendecompositions via randomized methods. 2023-06-16
defiant public Differential methylation, Easy, Fast, Identification and ANnoTation. 2023-06-16
matplotlib public Publication quality figures in Python 2023-06-16
tsne public TSNE implementations for Python. 2023-06-16
martian public Martian is a language and framework for developing and executing complex computational pipelines. 2023-06-16
gpm public GPM ("General Purpose Mouse") software provides support for mouse devices in Linux virtual consoles. 2023-06-16
midnight-commander public GNU Midnight Commander is a visual file manager, licensed under GNU General Public License and therefore qualifies as Free Software. It's a feature rich full-screen text mode application that allows you to copy, move and delete files and whole directory trees, search for files and run commands in the subshell. Internal viewer and editor are included. 2023-06-16
tcllib public This package is intended to be a collection of Tcl packages that provide utility functions useful to large collection of Tcl programmers. 2023-06-16
globusconnectpersonal public Globus Connect Personal 2023-06-16
maxquant public MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted. 2023-06-16
stockfish public Stockfish is a free, powerful UCI chess engine derived from Glaurung 2.1. 2023-06-16
justorthologs public JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. 2023-06-16
morgan public MORGAN is part of our software for Markov chain Monte Carlo in Genetic Analysis. 2023-06-16
jvarkit-vcf2bam public Converts VCF to BAM files 2023-06-16
mro-data.table public Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development. 2023-06-16
abacas public ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. 2023-06-16
gym public The OpenAI Gym: A toolkit for developing and comparing your reinforcement learning agents. 2023-06-16
pybullet public Official Python Interface for the Bullet Physics SDK specialized for Robotics Simulation and Reinforcement Learning 2023-06-16
phylophlan public PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. 2023-06-16
gdc-client public GDC Data Transfer Tool 2023-06-16
melonnpan public MelonnPan is a computational method for predicting metabolite compositions from shotgun metagenomic sequencing data. 2023-06-16
r-phylogic public Phylogenetic analysis of subclones across multiple cancer-tissue samples. 2023-06-16
azcopy public AzCopy is a command-line utility designed for copying data to/from Microsoft Azure Blob and File storage, using simple commands designed for optimal performance. 2023-06-16
titancna public Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer. 2023-06-16
sports1.0 public Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs. 2023-06-16
sandstone-spawner public JupyterHub Spawner class for starting Sandstone HPC user instances. 2023-06-16
batchspawner public This is modified batchspawner for Jupyterhub on HCC resources. 2023-06-16
sandstone-jupyterhub-login public This is modified JupyterHub multi-user spawner for Sandstone IDE on HCC resources. 2023-06-16
jupyter-duoauthenticator public Simple Duo Authenticator Plugin for JupyterHub. 2023-06-16
sandstone-slurm-assist public This is modified Slurm scheduler assist app for Sandstone IDE on HCC resources. 2023-06-16
duo_python public Duo two-factor authentication for Python web applications. 2023-06-16

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