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R-roxygen2-7.1.2-2.fc36.x86_64
Generate your Rd documentation, 'NAMESPACE' file, and collation field using specially formatted comments. Writing documentation in-line with code makes it easier to keep your documentation up-to-date as your requirements change. 'Roxygen2' is inspired by the 'Doxygen' system for C++.
Located in LBN / … / Big Data / BastionLinux 36
R-rprintf-0.2.1-2.lbn25.noarch
Provides a set of functions to facilitate building formatted strings under various replacement rules: C-style formatting, variable-based formatting, and number-based formatting. C-style formatting is basically identical to built-in function 'sprintf'. Variable-based formatting allows users to put variable names in a formatted string which will be replaced by variable values. Number-based formatting allows users to use index numbers to represent the corresponding argument value to appear in the string.
Located in LBN / … / Big Data / BastionLinux 25
R-rprintf-0.2.1-14.fc36.noarch
Provides a set of functions to facilitate building formatted strings under various replacement rules: C-style formatting, variable-based formatting, and number-based formatting. C-style formatting is basically identical to built-in function 'sprintf'. Variable-based formatting allows users to put variable names in a formatted string which will be replaced by variable values. Number-based formatting allows users to use index numbers to represent the corresponding argument value to appear in the string.
Located in LBN / … / Big Data / BastionLinux 36
R-rprojroot-1.2-2.lbn25.noarch
Robust, reliable and flexible paths to files below a project root. The 'root' of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.
Located in LBN / … / Big Data / BastionLinux 25
R-rprojroot-2.0.2-6.fc36.noarch
Robust, reliable and flexible paths to files below a project root. The 'root' of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.
Located in LBN / … / Big Data / BastionLinux 36
R-Rsamtools-1.24.0-1.lbn19.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.
Located in LBN / … / Big Data / BastionLinux 19
R-Rsamtools-1.28.0-3.lbn25.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.
Located in LBN / … / Big Data / BastionLinux 25
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.
Located in LBN / … / Big Data / BastionLinux 36
R-Rsolid-0.9.31-18.lbn19.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.
Located in LBN / … / Big Data / BastionLinux 19
R-Rsolid-0.9.31-22.lbn25.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.
Located in LBN / … / Big Data / BastionLinux 25

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