Package: single 1.9.0
Rocio Espada
single: Accurate consensus sequence from nanopore reads of a gene library
Accurate consensus sequence from nanopore reads of a DNA gene library. SINGLe corrects for systematic errors in nanopore sequencing reads of gene libraries and it retrieves true consensus sequences of variants identified by a barcode, needing only a few reads per variant. More information in preprint doi: https://doi.org/10.1101/2020.03.25.007146.
Authors:
single_1.9.0.tar.gz
single_1.9.0.zip(r-4.5)single_1.9.0.zip(r-4.4)single_1.9.0.zip(r-4.3)
single_1.9.0.tgz(r-4.4-any)single_1.9.0.tgz(r-4.3-any)
single_1.9.0.tar.gz(r-4.5-noble)single_1.9.0.tar.gz(r-4.4-noble)
single_1.9.0.tgz(r-4.4-emscripten)single_1.9.0.tgz(r-4.3-emscripten)
single.pdf |single.html✨
single/json (API)
| # Install 'single' in R: |
| install.packages('single', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- ascii_v - ASCII code
- bases - Bases
- mutation_rate - Mutation_rate
On BioConductor:single-1.9.0(bioc 3.20)single-1.7.0(bioc 3.19)
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:e9ba58a6f5
Exports:evaluate_fitsfit_logregrglm.predict.list_mismatchesp_prior_errorsp_prior_mutationspileup_by_QUALsingle_consensus_byBarcodesingle_evaluatesingle_trainweighted_consensus
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurlDelayedArraydplyrfansiformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyrpurrrR6Rcppreshape2RhtslibrlangRsamtoolsS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ASCII code | ascii_v |
| Bases | bases |
| Evaluate SINGLE fits | evaluate_fits |
| Fit SINGLE's logistic regression | fit_logregr |
| Computes prior probability of mutations | |
| Lists mismatches between two DNAstrings | list_mismatches |
| mutation_rate | mutation_rate |
| Computes prior probability of errors | p_prior_errors |
| Computes prior probability of mutations | p_prior_mutations |
| Pileup by QUAL | pileup_by_QUAL |
| Compute SINGLE consensus | single_consensus_byBarcode |
| Evaluate SINGLE model | single_evaluate |
| Train SINGLE model | single_train |
| Compute consensus sequence | weighted_consensus |
