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HCC / packages

Package Name Access Summary Updated
sniffles2-plot public Visualizer tool for plot generating 2024-10-25
hcc-jupyter-kernels public Jupyter kernelspec files for HCC resources 2024-10-18
compass-cplex public In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes. 2024-09-13
cnvcaller public CNVcaller is designed to detect copy number variation using sequencing data from populations. 2024-08-22
gsufsort public Building suffix arrays, LCP-arrays and BWTs for string collections. 2024-08-05
biser public Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies. 2024-07-31
seq public Seq — the bioinformatics module for Codon. 2024-07-30
codon public A high-performance, zero-overhead, extensible Python compiler using LLVM. 2024-07-30
duo-client public Reference client for Duo Security APIs 2024-07-29
freesasa-cli public Calculate solvent accessible surface areas of proteins 2024-07-25
juicer public A One-Click System for Analyzing Loop-Resolution Hi-C Experiments. 2024-07-24
autodock-gpu public AutoDock for GPUs using OpenCL. 2024-07-10
cudatoolkit public NVIDIA CUDA Toolkit 2024-07-10
afni public AFNI is a suite of programs for looking at and analyzing 3D brain images. 2024-07-03
mro public Microsoft R Open is the enhanced distribution of R from Microsoft Corporation. 2024-07-03
tensorflow-cpucompat public Computation using data flow graphs for scalable machine learning. 2024-07-03
dorado-gpu public Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 2024-06-26
dorado public Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 2024-06-26
mrtrix3tissue public MRtrix3Tissue adds capabilities for 3-Tissue CSD modelling and analysis to a complete version of MRtrix3. 2024-06-21
modflow-2005 public Three-dimensional finite-difference ground-water flow model. 2024-06-14
poplddecay public Fast and effective tool for linkage disequilibrium decay analysis. 2024-05-17
xcrysden public XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. 2024-05-14
tensorboard-plugin-profile public A profiling and performance analysis tool for TensorFlow. 2024-05-10
gviz-api public Python API for Google Visualization 2024-05-10
togl public A Tcl/Tk widget for OpenGL rendering. 2024-05-07
boa-bacfinder public Find bacteriocins in bacterial genomes 2024-04-28
deepemhancer public Deep learning for cryo-EM maps post-processing. 2024-04-25
tpg public Toy Parser Generator is a lexical and syntactic parser generator for Python. 2024-04-24
pysages public Python Suite for Advanced General Ensemble Simulations. 2024-04-23
dssp public Application to assign secondary structure to proteins. 2024-04-02
libmcfp public A header only library that can collect configuration options from command line arguments and configuration files. 2024-04-01
psipred public The PSIPRED Workbench provides a range of protein structure prediction methods. 2024-03-27
revbayes public Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language. 2024-02-29
consurf public Stand Alone version of ConSurf 2024-01-18
jmodeltest public jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. 2024-01-04
gurobi-matlab public MATLAB files for Gurobi optimizer. 2023-12-21
prottest3 public ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. 2023-12-20
rate4site public Rate4Site is a program for detecting conserved amino-acid sites by computing the relative evolutionary rate for each site in the multiple sequence alignment (MSA).. 2023-12-20
subversion public Enterprise-class centralized version control for the masses 2023-08-08
ashs public ASHS is software for automatic segmentation of the medial temporal lobe (MTL) substructures from brain MRI scans. 2023-08-01
shtns public SHTns is a high performance library for Spherical Harmonic Transform written in C, aimed at numerical simulation (fluid flows, mhd, ...) in spherical geometries. 2023-07-12
r-paran public An implementation of Horn's technique for numerically and graphically evaluating the components or factors retained in a principle components analysis (PCA) or common factor analysis (FA). Horn's method contrasts eigenvalues produced through a PCA or FA on a number of random data sets of uncorrelated variables with the same number of variables and observations as the experimental or observational data set to produce eigenvalues for components or factors that are adjusted for the sample error-induced inflation. Components with adjusted eigenvalues greater than one are retained. paran may also be used to conduct parallel analysis following Glorfeld's (1995) suggestions to reduce the likelihood of over-retention. 2023-07-06
r-phia public Analysis of terms in linear, generalized and mixed linear models, on the basis of multiple comparisons of factor contrasts. Specially suited for the analysis of interaction terms. 2023-07-06
cp2k public Quantum chemistry and solid state physics software package 2023-06-30
nquire public A statistical framework for ploidy estimation using NGS short-read data. 2023-06-22
git public distributed version control system 2023-06-18
popoolation2 public PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. 2023-06-18
t-coffee public A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence 2023-06-18
nomad public NOMAD is an unsupervised and reference-free unifying framework to discover regulated sequence variation through statistical analysis of k-mer composition in both DNA and RNA sequence. 2023-06-18
blobtoolkit public Interactive quality assessment of genome assemblies. 2023-06-18

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