Showing 20 of total 20 results (show query)
bioc
beadarray:Quality assessment and low-level analysis for Illumina BeadArray data
The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
Maintained by Mark Dunning. Last updated 5 months ago.
microarrayonechannelqualitycontrolpreprocessing
15.0 match 7.88 score 70 scripts 4 dependents
r-lib
devtools:Tools to Make Developing R Packages Easier
Collection of package development tools.
Maintained by Jennifer Bryan. Last updated 6 months ago.
5.1 match 2.4k stars 19.51 score 51k scripts 148 dependents
henrikbengtsson
port4me:Get the Same, Personal, Free 'TCP' Port over and over
An R implementation of the cross-platform, language-independent "port4me" algorithm (<https://github.com/HenrikBengtsson/port4me>), which (1) finds a free Transmission Control Protocol ('TCP') port in [1024,65535] that the user can open, (2) is designed to work in multi-user environments, (3), gives different users, different ports, (4) gives the user the same port over time with high probability, (5) gives different ports for different software tools, and (6) requires no configuration.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
bashclihigh-performance-computinghpcmulti-tenantmulti-userportpypi-packagepythonr-languager-programmingtcputility
11.0 match 13 stars 5.11 score 5 scriptsbioc
systemPipeR:systemPipeR: Workflow Environment for Data Analysis and Report Generation
systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.
Maintained by Thomas Girke. Last updated 5 months ago.
geneticsinfrastructuredataimportsequencingrnaseqriboseqchipseqmethylseqsnpgeneexpressioncoveragegenesetenrichmentalignmentqualitycontrolimmunooncologyreportwritingworkflowstepworkflowmanagement
4.5 match 53 stars 11.56 score 344 scripts 3 dependents
sagiegurari
scriptexec:Execute Native Scripts
Run complex native scripts with a single command, similar to system commands.
Maintained by Sagie Gur-Ari. Last updated 4 years ago.
bash-scriptscriptingshell-script
7.5 match 3 stars 4.50 score 21 scripts
devopifex
erratum:Handle Error and Warning Messages
Elegantly handle error and warning messages.
Maintained by John Coene. Last updated 1 years ago.
5.6 match 22 stars 3.04 score 5 scriptsbioc
derfinder:Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.
Maintained by Leonardo Collado-Torres. Last updated 3 months ago.
differentialexpressionsequencingrnaseqchipseqdifferentialpeakcallingsoftwareimmunooncologycoverageannotation-agnosticbioconductorderfinder
1.5 match 42 stars 10.03 score 78 scripts 6 dependents
mdplot
MDplot:Visualising Molecular Dynamics Analyses
Provides automatisation for plot generation succeeding common molecular dynamics analyses. This includes straightforward plots, such as RMSD (Root-Mean-Square-Deviation) and RMSF (Root-Mean-Square-Fluctuation) but also more sophisticated ones such as dihedral angle maps, hydrogen bonds, cluster bar plots and DSSP (Definition of Secondary Structure of Proteins) analysis. Currently able to load GROMOS, GROMACS and AMBER formats, respectively.
Maintained by Christian Margreitter. Last updated 3 years ago.
1.9 match 27 stars 6.46 score 36 scripts
mcanouil
eggla:Early Growth Genetics Longitudinal Analysis
Tools for longitudinal analysis within the EGG (Early Growth Genetics) Consortium (<http://egg-consortium.org/>).
Maintained by Mickaël Canouil. Last updated 1 months ago.
geneticsgrowth-curvesinfancylongitudinal-analysismixed-effects-modelsspline-regression
2.5 match 3 stars 4.15 score 19 scripts
rogiersbart
bro:My personal R tools
This package collects some functions I created for myself to facilitate certain tasks. I do not expect it to be very useful for anyone else, but if you think this can help you out, be my guest!
Maintained by Bart Rogiers. Last updated 7 months ago.
5.3 match 1.70 score 7 scripts
trevorld
bracer:Brace Expansions
Performs brace expansions on strings. Made popular by Unix shells, brace expansion allows users to concisely generate certain character vectors by taking a single string and (recursively) expanding the comma-separated lists and double-period-separated integer and character sequences enclosed within braces in that string. The double-period-separated numeric integer expansion also supports padding the resulting numbers with zeros.
Maintained by Trevor L Davis. Last updated 2 years ago.
1.9 match 2 stars 4.59 score 13 scripts 1 dependents
nicholasjcooper
NCmisc:Miscellaneous Functions for Creating Adaptive Functions and Scripts
A set of handy functions. Includes a versatile one line progress bar, one line function timer with detailed output, time delay function, text histogram, object preview, CRAN package search, simpler package installer, Linux command install check, a flexible Mode function, top function, simulation of correlated data, and more.
Maintained by Nicholas Cooper. Last updated 2 years ago.
1.7 match 3.86 score 172 scripts 5 dependents
inbo
n2kanalysis:Generic Functions to Analyse Data from the 'Natura 2000' Monitoring
All generic functions and classes for the analysis for the 'Natura 2000' monitoring. The classes contain all required data and definitions to fit the model without the need to access other sources. Potentially they might need access to one or more parent objects. An aggregation object might for example need the result of an imputation object. The actual definition of the analysis, using these generic function and classes, is defined in dedictated analysis R packages for every monitoring scheme. For example 'abvanalysis' and 'watervogelanalysis'.
Maintained by Thierry Onkelinx. Last updated 1 months ago.
1.8 match 1 stars 3.18 score 7 scripts
narenschandran
scriptloc:Get the Location of the R Script that is Being Sourced/Executed
Provides functions to retrieve the location of R scripts loaded through the source() function or run from the command line using the Rscript command. This functionality is analogous to the Bash shell's ${BASH_SOURCE[0]}. Users can first set the project root's path relative to the script path and then all subsequent paths relative to the root. This system ensures that all paths lead to the same location regardless of where any script is executed/loaded from without resorting to the use of setwd() at the top of the scripts.
Maintained by Naren Chandran Sakthivel. Last updated 2 years ago.
2.0 match 2.70 score 6 scripts
leef-uzh
LEEF:Data Package Containing Only Data and Data Information
Setup package for the LEEF pipeline which loads / installs all necessary packages and functions to run the pipeline.
Maintained by Rainer M. Krug. Last updated 3 years ago.
data-analysisdata-processingleef
1.5 match 2.95 score
cran
vmr:Virtual Machines for R
Manage, provision and use Virtual Machines pre-configured for R. Develop, test and build package in a clean environment. 'Vagrant' tool and a provider (such as 'Virtualbox') have to be installed.
Maintained by Jean-François Rey. Last updated 2 years ago.
1.2 match 3.65 scorecran
varitas:Variant Calling in Targeted Analysis Sequencing Data
Multi-caller variant analysis pipeline for targeted analysis sequencing (TAS) data. Features a modular, automated workflow that can start with raw reads and produces a user-friendly PDF summary and a spreadsheet containing consensus variant information.
Maintained by Adam Mills. Last updated 4 years ago.
1.7 match 2.30 scorecran
cgwtools:Miscellaneous Tools
Functions for performing quick observations or evaluations of data, including a variety of ways to list objects by size, class, etc. The functions 'seqle' and 'reverse.seqle' mimic the base 'rle' but can search for linear sequences. The function 'splatnd' allows the user to generate zero-argument commands without the need for 'makeActiveBinding' . Functions provided to convert from any base to any other base, and to find the n-th greatest max or n-th least min. In addition, functions which mimic Unix shell commands, including 'head', 'tail' ,'pushd' ,and 'popd'. Various other goodies included as well.
Maintained by Carl Witthoft. Last updated 1 years ago.
3.6 match 1.00 score
jdhayes
RenvModule:Interface to Allow Full Use of the Environment Modules System for Unix
Provides environment modules functionality, which enables use of the Environment Modules system (<http://modules.sourceforge.net/>) from within the R environment. By default the user's login shell environment (ie. "bash -l") will be used to initialize the current session. The module function can also; load or unload specific software, list all the loaded software within the current session, and list all the applications available for loading from the module system. Lastly, the module function can remove all loaded software from the current session.
Maintained by Jordan Hayes. Last updated 3 years ago.
0.5 match 2 stars 3.00 score 1 scripts