No packages match

illuminaio - Parsing Illumina Microarray Output Files

Tools for parsing Illumina's microarray output files, including IDAT.

Last updated

infrastructuredataimportmicroarrayproprietaryplatformsbioconductor

9.87 score 5 stars 40 dependents 1 scripts 8.9k downloads

affxparser - Affymetrix File Parsing SDK

Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

Last updated

infrastructuredataimportmicroarrayproprietaryplatformsonechannelbioconductorcpp

8.68 score 8 stars 15 dependents 91 scripts 3.7k downloads

progressify - Progress Reporting of Common Functions via One Magic Function

The progressify() function rewrites (transpiles) calls to sequential and parallel map-reduce functions such as base::lapply(), purrr::map(), foreach::foreach(), and plyr::llply() to signal progress updates. By combining this function with R's native pipe operator, you have a straightforward way to report progress on iterative computations with minimal refactoring, e.g. 'lapply(x, fcn) |> progressify()' and 'purrr::map(x, fcn) |> progressify()'. It is compatible with the parallel-processing map-reduce packages 'future.apply', 'furrr', 'crossmap', 'foreach', 'doFuture', and 'futurize'. It also supports domain-specific packages including 'boot', 'fwb', 'lme4', 'partykit', 'sandwich', and 'SimDesign', e.g. 'boot::boot(data, stat, R) |> progressify()'.

Last updated

futureverseprogresstranspiler

7.55 score 5 stars 63 scripts 422 downloads

aroma.light - Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

Last updated

infrastructuremicroarrayonechanneltwochannelmultichannelvisualizationpreprocessingbioconductor

6.33 score 1 stars 15 dependents 28 scripts 2.9k downloads

future.p2p - A Peer-to-Peer Compute Cluster via Futureverse

Implementation of the 'Future' API <doi:10.32614/RJ-2021-048> that resolves futures on a peer-to-peer ('P2P') compute environment. By using this future backend, you and your friends can share your spare compute resources with each other.

Last updated

distributed-computingfuturefutureversep2pparallelparallel-computing

5.68 score 16 stars 4 scripts

marshal - Framework to Marshal Objects to be Used in Another R Process

Some types of R objects can be used only in the R session they were created. If used as-is in another R process, such objects often result in an immediate error or in obscure and hard-to-troubleshoot outcomes. Because of this, they cannot be saved to file and re-used at a later time. They can also not be exported to a worker in parallel processing. These objects are sometimes referred to as non-exportable or non-serializable objects. One solution to this problem is to use "marshalling" to encode the R object into an exportable representation that then can be used to re-create a copy of that object in another R process. This package provides a framework for marshalling and unmarshalling R objects such that they can be transferred using functions such as serialize() and unserialize() of base R.

Last updated

marshallingparallelserialization

3.13 score 15 stars 18 scripts

seguid - Sequence Globally Unique Identifier (SEGUID) Checksums

Implementation of the original Sequence Globally Unique Identifier (SEGUID) algorithm [Babnigg and Giometti (2006) <doi:10.1002/pmic.200600032>] and SEGUID v2 (<https://www.seguid.org>), which extends SEGUID v1 with support for linear, circular, single- and double-stranded biological sequences, e.g. DNA, RNA, and proteins.

Last updated

seguid

2.70 score 5 scripts 217 downloads

dChipIO - Methods for Reading dChip Files

Functions for reading DCP and CDF.bin files generated by the dChip software.

Last updated

infrastructuredataimport

2.70 score 3 scripts 241 downloads

AffymetrixDataTestFiles - Affymetrix Data Files (CEL, CDF, CHP, EXP, PGF, PSI) for Testing

This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix' Fusion SDK distribution and other official sources.

Last updated

experimentdatamicroarraydatadatapkg

2.30 score

future.tools - Tools for Working with Futures

Tools for Working with Futures.

Last updated

parallel-computingparallel-programming

2.00 score 1 stars

doFuture.tests.extra - Extra Test Sets for the 'doFuture' Package

Runs examples of packages that use 'foreach' and '%dopar%' for parallelization, where 'doFuture' is used as the 'foreach' adapter making it possible to use any future backend for parallelization. The package tests use these tools to test 'doFuture' with 'foreach'-based examples from packages 'BiocParallel', 'caret', 'doParallel', 'glmnet', 'NMF', 'plyr', and 'TSP'. These tests are run with many known future backends.

Last updated

futureverseparalleltestsuite

1.70 score

HaarSeg - Fast and Flexible Microarray Segmentation

A fast and flexible method for the segmentation of aCGH data using the HaarSeg method by Ben-Yaacov and Eldar (2008) <doi:10.1093/bioinformatics/btn272>.

Last updated

legacy

1.70 score

expectile - Modelling of Expectiles

Methods for fitting a simplex or polyhedral cone to multivariate data, for doing expectile regression and skyline/baseline estimation.

Last updated

1.70 score

sfit - Multidimensional Simplex Fitting

Methods for robustly fitting a K-dimensional simplex in M dimensions.

Last updated

cconemodelsimplex

1.70 score 1 stars