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illuminaio - Parsing Illumina Microarray Output Files

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

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infrastructuredataimportmicroarrayproprietaryplatformsbioconductor

10.57 score 5 stars 39 dependents 93 scripts 4.8k 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.

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infrastructuredataimportmicroarrayproprietaryplatformsonechannelbioconductorcpp

8.81 score 8 stars 14 dependents 88 scripts 3.2k 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.

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infrastructuremicroarrayonechanneltwochannelmultichannelvisualizationpreprocessingbioconductor

6.27 score 1 stars 14 dependents 27 scripts 2.8k 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.

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distributed-computingfuturefutureversep2pparallelparallel-computing

5.77 score 15 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.

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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.

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seguid

2.70 score 5 scripts 210 downloads

dChipIO - Methods for Reading dChip Files

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

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infrastructuredataimport

2.70 score 3 scripts 188 downloads

future.tools - Tools for Working with Futures

Tools for Working with Futures.

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parallel-computingparallel-programming

2.00 score 1 stars 3 scripts

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.

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futureverseparalleltestsuite

1.70 score

ictml - Easily Install and Load the 'ICTML'

The 'ICTML' is a software suite implementing the Interpretable Causal Targeted Machine Learning ('ICTML') Project <https://www.ictml.org>.

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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>.

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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.

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1.70 score

sfit - Multidimensional Simplex Fitting

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

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cconemodelsimplex

1.70 score 1 stars