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newt
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public |
No Summary
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2023-06-16 |
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optitype
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public |
Precision HLA typing from next-generation sequencing data
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2023-06-16 |
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r-snow
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public |
Support for simple parallel computing in R.
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2023-06-16 |
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test-glibc
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public |
Find which glibc version is used for building packages.
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2023-06-16 |
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vawk
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public |
An awk-like VCF parser
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2023-06-16 |
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r-rappdirs
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public |
An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's Appdirs (\url{https://github.com/ActiveState/appdirs}) to R.
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2023-06-16 |
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hmmlearn
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public |
Hidden Markov Models in Python, with scikit-learn like API
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2023-06-16 |
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msms
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public |
MSMS is a program written in the C programming language to compute molecular surfaces.
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2023-06-16 |
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r-optparse
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public |
A command line parser inspired by Python's 'optparse' library to be used with Rscript to write "#!" shebang scripts that accept short and long flag/options.
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2023-06-16 |
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knot
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public |
Detection of knots in protein folds.
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2023-06-16 |
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r-getoptlong
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public |
This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.
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2023-06-16 |
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pyomo
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public |
Pyomo: Python Optimization Modeling Objects
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2023-06-16 |
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gfold
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public |
Find differentially expressed genes from RNA-seq data with few replicates using generalized fold changes.
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2023-06-16 |
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bleach
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public |
An easy whitelist-based HTML-sanitizing tool.
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2023-06-16 |
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moreutils
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public |
a growing collection of the unix tools that nobody thought to write long ago when unix was young
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2023-06-16 |
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xmltodict
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public |
Makes working with XML feel like you are working with JSON
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2023-06-16 |
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urllib3
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public |
HTTP library with thread-safe connection pooling, file post, and more.
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2023-06-16 |
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httpretty
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public |
HTTP client mock for Python
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2023-06-16 |
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r-fda
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public |
These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer. They were ported from earlier versions in Matlab and S-PLUS. An introduction appears in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009) Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. Matlab versions of the code and sample analyses are no longer distributed through CRAN, as they were when the book was published. For those, ftp from http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/ There you find a set of .zip files containing the functions and sample analyses, as well as two .txt files giving instructions for installation and some additional information. The changes from Version 2.4.1 are fixes of bugs in density.fd and removal of functions create.polynomial.basis, polynompen, and polynomial. These were deleted because the monomial basis does the same thing and because there were errors in the code.
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2023-06-16 |
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toposort
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public |
A topological sort algorithm for Python.
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2023-06-16 |
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r-ggally
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public |
GGally is designed to be a helper to ggplot2. It contains templates for different plots to be combined into a plot matrix, a parallel coordinate plot function, as well as a function for making a network plot.
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2023-06-16 |
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xsv
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public |
A fast CSV toolkit written in Rust.
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2023-06-16 |
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r-futile.logger
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public |
Provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.
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2023-06-16 |
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ngs-sdk
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public |
NGS SDK Language Bindings
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2023-06-16 |
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r-catools
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public |
Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.
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2023-06-16 |
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sure
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public |
utility belt for automated testing in python for python
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2023-06-16 |
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confindr
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public |
Detect intra- and inter-species bacterial contamination in NGS reads
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2023-06-11 |
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dfam
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public |
The Dfam database is a collection of Repetitive DNA element sequence alignments, hidden Markov models (HMMs) and matches lists for complete Eukaryote genomes
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2023-06-08 |
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isoseq3
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public |
Iso-Seq - Scalable De Novo Isoform Discovery
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2023-06-07 |
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epicseg
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public |
EpiCSeg (Epigenome Count-based Segmentation) is a software for annotating the genome based on the state of the chromatin. It provides tools for extracting count data from BAM files, typlically corresponding to ChIP-seq experiments for histone marks (but other choices are possible) it learns a statistical model for the read counts based on a HMM, it annotates the genome, and it provides tools for displaying and analyzing the obtained models and segmentations. EpiCSeg can be used as an R package or from the command line via Rscript.
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2023-06-01 |
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plastid
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public |
plastid is a Python library for genomic analysis -- in particular, high-throughput sequencing data
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2023-05-31 |
