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gdc-client
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public |
GDC Data Transfer Tool
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2025-03-25 |
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azcopy
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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.
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2025-03-25 |
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titancna
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public |
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer.
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2025-03-25 |
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sports1.0
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public |
Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs.
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2025-03-25 |
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sandstone-spawner
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public |
JupyterHub Spawner class for starting Sandstone HPC user instances.
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2025-03-25 |
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sandstone-slurm-assist
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public |
This is modified Slurm scheduler assist app for Sandstone IDE on HCC resources.
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2025-03-25 |
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sandstone-jupyterhub-login
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public |
This is modified JupyterHub multi-user spawner for Sandstone IDE on HCC resources.
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2025-03-25 |
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jupyter-duoauthenticator
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public |
Simple Duo Authenticator Plugin for JupyterHub.
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2025-03-25 |
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sandstone-ide
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public |
This is modified Sandstone IDE for HCC resources.
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2025-03-25 |
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wrapspawner
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public |
Mechanism for runtime configuration of spawners for JupyterHub.
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2025-03-25 |
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batchspawner
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public |
This is modified batchspawner for Jupyterhub on HCC resources.
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2025-03-25 |
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hcc-du
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public |
HCC utility to query quota and file purge status.
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2025-03-25 |
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duo_python
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public |
Duo two-factor authentication for Python web applications.
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2025-03-25 |
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simplepam
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public |
An interface to the Pluggable Authentication Modules (PAM) library on linux, written in pure python (using ctypes).
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2025-03-25 |
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bitmath
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public |
Pythonic module for representing and manipulating file sizes with different prefix notations (file size unit conversion).
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2025-03-25 |
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r-phia
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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.
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2025-03-25 |
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r-paran
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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.
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2025-03-25 |
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lyve-set
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public |
LYVE version of the Snp Extraction Tool (SET), a method of using hqSNPs to create a phylogeny.
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2025-03-25 |
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lyve-set-cg-pipeline
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public |
Genome assembly/prediction/annotation pipeline for the Linux command line
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2025-03-25 |
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mni-n3
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public |
A non-parametric method for correction of intensity non-uniformity in MRI data.
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2025-03-25 |
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perl-getopt-tabular
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public |
table-driven argument parsing for Perl 5
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2025-03-25 |
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perl-mni
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public |
The MNI Perl Library is a collection of Perl modules originally designed to help writing glorified shell scripts -- that is, programs that (mainly) run other programs.
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2025-03-25 |
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perl-schedule-sgelk
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public |
Perl module for scheduling tasks, with only using qsub/qstat/qdel.
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2025-03-25 |
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perl-statistics-linefit
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public |
Least squares line fit, weighted or unweighted
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2025-03-25 |
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perl-graph-centrality-pagerank
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public |
Computes pagerank of all nodes in a graph.
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2025-03-25 |
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perl-array-intspan
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public |
Handles arrays of scalars or objects using integer ranges
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2025-03-25 |
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ebtks
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public |
EBTKS - stands for Everything But The Kitchen Sink - is Alex Zijdenbos library of numerical types and algorithms, and is needed by classify and inormalize.
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2025-03-25 |
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boltztrap2
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public |
BoltzTraP2 is a modern implementation of the smoothed Fourier interpolation algorithm for electronic bands that formed the base of the original and widely used BoltzTraP code.
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2025-03-25 |
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srtools
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public |
srtools is the toolkit used by members of the Carrington lab for processing and analyzing small RNA sequencing data.
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2025-03-25 |
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r-udpipe
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public |
This natural language processing toolkit provides language-agnostic 'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency parsing' of raw text. Next to text parsing, the package also allows you to train annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided at <http://universaldependencies.org/format.html>. The techniques are explained in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0 with UDPipe', available at <doi:10.18653/v1/K17-3009>.
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2025-03-25 |
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pyemto
|
public |
Easily generate input files and corresponding batch scripts for the EMTO (Exact Muffin-Tin Orbitals) solid-state physics software.
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2025-03-25 |
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pymatgen
|
public |
Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes.
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2025-03-25 |
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cif2cell-python3
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public |
CIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file.
|
2025-03-25 |
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llvm-dynlib
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public |
The LLVM Compiler Infrastructure
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2025-03-25 |
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ima3
|
public |
IMa3 provides for estimation of the posterior probability of the population phylogenetic topology by using a new kind of data augmentation called a 'hidden genealogy'.
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2025-03-25 |
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tensorflow-probability
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public |
TensorFlow Probability is a library for probabilistic reasoning and statistical analysis.
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2025-03-25 |
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gurobi-python
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public |
The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
|
2025-03-25 |
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plink2
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public |
This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab at Mount Sinai School of Medicine, and others.
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2025-03-25 |
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rclone
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public |
Rclone - rsync for cloud storage.
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2025-03-25 |
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doom-py
|
public |
Python wrappers for ViZDoom. Contains a modified version of the bleeding-edge ViZDoom source code.
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2025-03-25 |
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seqtk
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public |
This is modified Seqtk version required for FusionCatcher.
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2025-03-25 |
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mlpack
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public |
mlpack a fast, flexible machine learning library
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2025-03-25 |
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armadillo
|
public |
Armadillo C++ linear algebra library
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2025-03-25 |
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neper
|
public |
Neper is a software package for polycrystal generation and meshing.
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2025-03-25 |
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libmatheval
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public |
GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
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2025-03-25 |
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guile
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public |
Guile is designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts.
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2025-03-25 |
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gensel
|
public |
Genomic selection and GWAS analysis for linear and categorical traits.
|
2025-03-25 |
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libgc
|
public |
The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.
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2025-03-25 |
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project-lazarus
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public |
Lazarus is a collection of Python scripts for running the programs codeml and baseml in the PAML software suite.
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2025-03-25 |
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mro-tidyverse
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public |
The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step. Learn more about the 'tidyverse' at <https://tidyverse.org>.
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2025-03-25 |
