Package: sagenhaft 1.77.0
Tim Beissbarth
sagenhaft: Collection of functions for reading and comparing SAGE libraries
This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts.
Authors:
sagenhaft_1.77.0.tar.gz
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sagenhaft.pdf |sagenhaft.html✨
sagenhaft/json (API)
| # Install 'sagenhaft' in R: |
| install.packages('sagenhaft', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- SAGEartifacts - Functions for SAGE library extraction
On BioConductor:sagenhaft-1.77.0(bioc 3.21)sagenhaft-1.76.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:ac3f6cc311. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | WARNING | Dec 19 2024 |
| R-4.5-linux | WARNING | Dec 19 2024 |
| R-4.4-win | WARNING | Dec 19 2024 |
| R-4.4-mac | WARNING | Dec 19 2024 |
| R-4.3-win | WARNING | Dec 19 2024 |
| R-4.3-mac | WARNING | Dec 19 2024 |
Exports:combine.libscompare.lib.paircompute.sequence.neighborscompute.unique.tagscreate.matrix.csrdifference.scatter.plotem.estimate.error.givenestimate.errors.meanextract.ditagsextract.lib.from.directoryextract.lib.from.zipextract.library.tagsplot.sage.libraryplot.sage.library.comparisonprint.sage.libraryprint.sage.library.comparisonread.phd.fileread.sage.libraryread.sage.library.comparisonread.seq.qual.filepairreestimate.lib.from.tagcountsremove.sage.artifactsrevcompsage.testsagelibrary.simulatesummary.sage.librarysummary.sage.library.comparisontable.sparsetagmatrix2tagnumtagnum2tagmatrixtagnum2tagsequencetagsequence2tagnumwrite.sage.librarywrite.sage.library.comparison
Dependencies:SparseM
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Estimate sequencing errors and compute corrected counts | compute.sequence.neighbors em.estimate.error.given estimate.errors.mean |
| Functions for SAGE library extraction | combine.libs compute.unique.tags extract.ditags extract.lib.from.directory extract.lib.from.zip extract.library.tags read.phd.file read.seq.qual.filepair reestimate.lib.from.tagcounts remove.sage.artifacts SAGEartifacts |
| Class sage.library | plot.sage.library print.sage.library read.sage.library summary.sage.library write.sage.library |
| Class sage.library.comparison | compare.lib.pair plot.sage.library.comparison print.sage.library.comparison read.sage.library.comparison summary.sage.library.comparison write.sage.library.comparison |
| Compare Two SAGE Libraries | sage.test |
| Utilities | create.matrix.csr difference.scatter.plot revcomp table.sparse tagmatrix2tagnum tagnum2tagmatrix tagnum2tagsequence tagsequence2tagnum |
| Simulate SAGE libraries | sagelibrary.simulate |