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R-Rsamtools-2.8.0-3.fc36.x86_64
This package provides an interface to the 'samtools', 'bcftools',
and 'tabix' utilities (see 'LICENCE') for manipulating SAM
(Sequence Alignment / Map), binary variant call (BCF) and
compressed indexed tab-delimited (tabix) files.
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R-Rsolid-0.9.31-38.fc36.x86_64
Rsolid is an R package for normalizing fluorescent intensity data from
ABI/SOLiD second generation sequencing platform. It has been observed
that the color-calls provided by factory software contain technical
artifacts, where the proportions of colors called are extremely
variable across sequencing cycles. Under the random DNA fragmentation
assumption, these proportions should be equal across sequencing cycles
and proportional to the dinucleotide frequencies of the sample.
Rsolid implements a version of the quantile normalization algorithm
that transforms the intensity values before calling colors. Results
show that after normalization, the total number of mappable reads
increases by around 5%, and number of perfectly mapped reads increases
by 10%. Moreover a 2-5% reduction in overall error rates is observed,
with a 2-6% reduction in the rate of valid adjacent color
mis-matches. The latter is important, since it leads to a decrease in
false-positive SNP calls.
The normalization algorithm is computationally efficient. In a test we
are able to process 300 million reads in 2 hours using 10 computer
cluster nodes. The engine functions of the package are written in C
for better performance.
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R-S4Vectors-0.30.0-3.fc36.x86_64
The S4Vectors package defines the Vector and List virtual classes and a set of
generic functions that extend the semantic of ordinary vectors and lists in R.
Package developers can easily implement vector-like or list-like objects as
concrete subclasses of Vector or List. In addition, a few low-level concrete
subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented
in the S4Vectors package itself (many more are implemented in the IRanges
package and in other Bioconductor infrastructure packages).
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R-SummarizedExperiment-1.22.0-3.fc36.noarch
The SummarizedExperiment container contains one or more assays, each
represented by a marix-like object of numeric or other mode. The rows
typically represent genomic ranges of interest and the columns represent
samples.
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R-TH-data-1.0.10-8.fc35.noarch
Data for other R packages.
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R-V8-3.4.2-4.fc36.x86_64
An R interface to V8: Google's open source JavaScript and WebAssembly engine.
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R-XML-3.99.0.6-3.fc36.x86_64
Many approaches for both reading and creating XML (and HTML) documents
(including DTDs), both local and accessible via HTTP or FTP. Also offers
access to an XPath "interpreter".
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R-XVector-0.32.0-3.fc36.x86_64
Memory efficient S4 classes for storing sequences "externally" (behind an R
external pointer, or on disk).
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R-abind-1.4.5-12.fc36.noarch
Combine multi-dimensional arrays. This is a generalization of cbind and rbind.
Takes a sequence of vectors, matrices, or arrays and produces a single array
of the same or higher dimension.
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R-acepack-1.4.1-18.fc36.x86_64
ACE and AVAS (additivity and variance stabilization) are used to estimate
transformations for regression.
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