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qcli
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public |
qcli
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2023-06-16 |
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py-graphviz
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public |
Simple Python interface for Graphviz
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2023-06-16 |
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google-api-python-client
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public |
No Summary
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2023-06-16 |
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chanjo
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public |
Coverage analysis tool for clinical sequencing
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2023-06-16 |
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r-pcapp
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public |
Robust PCA by Projection Pursuit
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2023-06-16 |
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perl-module-build
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public |
Build and install Perl modules
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2023-06-16 |
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perl-bio-db-sam
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public |
Read SAM/BAM database files
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2023-06-16 |
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perl-vcftools-vcf
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public |
cpanm ready distribution of VCFtools Perl libraries
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2023-06-16 |
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protrac
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public |
piRNA detection
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2023-06-16 |
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glpk
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public |
The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
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2023-06-16 |
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jamm
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public |
JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately.
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2023-06-16 |
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variant-effect-predictor
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public |
The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
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2023-06-16 |
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prinseq
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public |
PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data
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2023-06-16 |
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perl-db-file
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public |
Perl5 access to Berkeley DB version 1.x.
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2023-06-16 |
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perl-app-cpanminus
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public |
get, unpack, build and install modules from CPAN
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2023-06-16 |
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lumpy-sv
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public |
a general probabilistic framework for structural variant discovery
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2023-06-16 |
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bio-vcf
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public |
Smart VCF parser
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2023-06-16 |
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hubward
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public |
Manage the visualization of large amounts of other people's [often messy] genomics data
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2023-06-16 |
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vispr
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public |
VISPR is a visualization framework and analysis workflow for CRISPR/Cas9 knockout screens. VISPR is designed to display results calculated by MAGeCK.
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2023-06-16 |
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r-listenv
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public |
List environments are environments that can be indexed similarly to lists, e.g. 'x <- listenv(); x[[2]] <- "b"; names(x)[2] <- "B"; print(x$B)'.
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2023-06-16 |
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r-circlize
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public |
Circular layout is an efficient way for the visualization of huge amounts of information. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.
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2023-06-16 |
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r-rcircos
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public |
A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.
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2023-06-16 |
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r-r.methodss3
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public |
Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods.
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2023-06-16 |
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r-cghflasso
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public |
Spatial smoothing and hot spot detection using the fused lasso regression
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2023-06-16 |
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bcbio-rnaseq
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public |
Report generation for bcbio-nextgen RNA-seq runs
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2023-06-16 |
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r-hwriter
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public |
Easy-to-use and versatile functions to output R objects in HTML format
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2023-06-16 |
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r-hdrcde
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public |
Computation of highest density regions in one and two dimensions, kernel estimation of univariate density functions conditional on one covariate, and multimodal regression.
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2023-06-16 |
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r-ggdendro
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public |
This is a set of tools for dendrograms and tree plots using 'ggplot2'. The 'ggplot2' philosophy is to clearly separate data from the presentation. Unfortunately the plot method for dendrograms plots directly to a plot device without exposing the data. The 'ggdendro' package resolves this by making available functions that extract the dendrogram plot data. The package provides implementations for tree, rpart, as well as diana and agnes cluster diagrams.
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2023-06-16 |
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r-pheatmap
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public |
Implementation of heatmaps that offers more control over dimensions and appearance.
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2023-06-16 |
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r-globals
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public |
Identifies global ("unknown") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.
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2023-06-16 |
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r-r.cache
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public |
Memoization can be used to speed up repetitive and computational expensive function calls. The first time a function that implements memoization is called the results are stored in a cache memory. The next time the function is called with the same set of parameters, the results are momentarily retrieved from the cache avoiding repeating the calculations. With this package, any R object can be cached in a key-value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).
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2023-06-16 |
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r-r.utils
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public |
Utility functions useful when programming and developing R packages.
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2023-06-16 |
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r-lsd
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public |
Create lots of colorful plots in a plethora of variations (try the LSD demotour() )
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2023-06-16 |
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elasticluster
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public |
Create, manage and setup computing clusters hosted on a public or private cloud infrastructure.
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2023-06-16 |
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r-locfit
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public |
Local regression, likelihood and density estimation.
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2023-06-16 |
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r-ade4
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public |
Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007)
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2023-06-16 |
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voluptuous
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public |
Python data validation library
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2023-06-16 |
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r-writexls
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public |
Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX) files from one or more data frames. Each data frame will be written to a separate named worksheet in the Excel spreadsheet. The worksheet name will be the name of the data frame it contains or can be specified by the user.
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2023-06-16 |
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r-shape
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public |
Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...
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2023-06-16 |
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fadapa
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public |
FAstqc DAta PArser - A minimal parser to parse FastQC output data
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2023-06-16 |
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oauth2client
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public |
client library for OAuth 2.0
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2023-06-16 |
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r-funr
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public |
A small utility which wraps Rscript and provides access to all R functions from the shell.
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2023-06-16 |
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r-params
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public |
An interface to simplify organizing parameters used in a package, using external configuration files. This attempts to provide a cleaner alternative to options().
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2023-06-16 |
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r-seqinr
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public |
Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Seqinr includes utilities for sequence data management under the ACNUC system described in Gouy, M. et al. (1984) Nucleic Acids Res. 12:121-127 <doi:10.1093/nar/12.1Part1.121>.
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2023-06-16 |
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r-nozzle.r1
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public |
The Nozzle package provides an API to generate HTML reports with dynamic user interface elements based on JavaScript and CSS (Cascading Style Sheets). Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big data sets. The package can be applied to any project where user-friendly reports need to be created.
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2023-06-16 |
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r-dunn.test
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public |
Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks.
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2023-06-16 |
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r-r.oo
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public |
Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
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2023-06-16 |
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r-statmod
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public |
No Summary
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2023-06-16 |
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r-matrixstats
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public |
High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedians().
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2023-06-16 |
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r-mclust
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public |
Normal Mixture Modelling fitted via EM algorithm for Model-Based Clustering, Classification, and Density Estimation, including Bayesian regularization.
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2023-06-16 |
