Package: FastqCleaner 1.25.0
Leandro Roser
FastqCleaner: A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
An interactive web application for quality control, filtering and trimming of FASTQ files. This user-friendly tool combines a pipeline for data processing based on Biostrings and ShortRead infrastructure, with a cutting-edge visual environment. Single-Read and Paired-End files can be locally processed. Diagnostic interactive plots (CG content, per-base sequence quality, etc.) are provided for both the input and output files.
Authors:
FastqCleaner_1.25.0.tar.gz
FastqCleaner_1.25.0.zip(r-4.5)FastqCleaner_1.25.0.zip(r-4.4)FastqCleaner_1.25.0.zip(r-4.3)
FastqCleaner_1.25.0.tgz(r-4.4-x86_64)FastqCleaner_1.25.0.tgz(r-4.4-arm64)FastqCleaner_1.25.0.tgz(r-4.3-x86_64)FastqCleaner_1.25.0.tgz(r-4.3-arm64)
FastqCleaner_1.25.0.tar.gz(r-4.5-noble)FastqCleaner_1.25.0.tar.gz(r-4.4-noble)
FastqCleaner_1.25.0.tgz(r-4.4-emscripten)FastqCleaner_1.25.0.tgz(r-4.3-emscripten)
FastqCleaner.pdf |FastqCleaner.html✨
FastqCleaner/json (API)
NEWS
| # Install 'FastqCleaner' in R: |
| install.packages('FastqCleaner', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:FastqCleaner-1.23.0(bioc 3.20)FastqCleaner-1.22.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
qualitycontrolsequencingsoftwaresangerseqsequencematching
Last updated 23 days agofrom:2a9505045e. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | NOTE | Oct 30 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 31 2024 |
| R-4.3-win-x86_64 | NOTE | Oct 30 2024 |
| R-4.3-mac-x86_64 | NOTE | Oct 31 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 31 2024 |
Exports:adapter_filtercheck_encodingcomplex_filterfixed_filterinject_letter_randomlaunch_fqclength_filtern_filterqmean_filterrandom_lengthrandom_qualrandom_seqseq_filterseq_namestrim3q_filterunique_filter
Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbslibcachemclicodetoolscommonmarkcpp11crayoncrosstalkcurlDelayedArraydeldirdigestDTevaluatefastmapfontawesomeformatRfsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehighrhtmltoolshtmlwidgetshttpuvhttrhwriterinterpIRangesjpegjquerylibjsonliteknitrlambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpngpromisespwalignR6rappdirsRColorBrewerRcppRcppEigenRhtslibrlangrmarkdownRsamtoolsS4ArraysS4VectorssassshinyshinyBSShortReadsnowsourcetoolsSparseArraySummarizedExperimentsystinytexUCSC.utilswithrxfunxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Remove full and partial adapters from a ShortReadQ object | adapter_filter |
| Check quality encoding | check_encoding |
| Remove sequences with low complexity | complex_filter |
| Remove a fixed number of bases of a ShortReadQ object from 3' or 5' | fixed_filter |
| Inject a letter in a set of sequences at random positions | inject_letter_random |
| Launch FastqCleaner application | launch_fqc |
| Filter sequences of a FASTQ file by length | length_filter |
| Remove sequences with non-identified bases (Ns) from a ShortReadQ object | n_filter |
| Filter sequences by their average quality | qmean_filter |
| Create a named object with random sequences and qualities | random_length |
| Create random qualities for a given encoding | random_qual |
| Create random sequences | random_seq |
| Remove a set of sequences | seq_filter |
| Create sequences names | seq_names |
| Filter sequences with low quality in 3' tails | trim3q_filter |
| Remove duplicated sequences in a FASTQ file | unique_filter |
