Launching the application | Description of the application | First panel | Selecting operations | Loading files | Advanced options | Second panel | Third panel | A worked example: FASTQ processing in a nutshell | Advanced use of the package | Main functions | Auxiliary functions | Contact information
Package: FastqCleaner 1.31.0
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_1.31.0.tar.gz
FastqCleaner_1.31.0.zip(r-4.7)FastqCleaner_1.31.0.zip(r-4.6)FastqCleaner_1.31.0.zip(r-4.5)
FastqCleaner_1.31.0.tgz(r-4.6-x86_64)FastqCleaner_1.31.0.tgz(r-4.6-arm64)FastqCleaner_1.31.0.tgz(r-4.5-x86_64)FastqCleaner_1.31.0.tgz(r-4.5-arm64)
FastqCleaner_1.31.0.tar.gz(r-4.7-arm64)FastqCleaner_1.31.0.tar.gz(r-4.7-x86_64)FastqCleaner_1.31.0.tar.gz(r-4.6-arm64)FastqCleaner_1.31.0.tar.gz(r-4.6-x86_64)
FastqCleaner_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FastqCleaner/json (API)
| # Install 'FastqCleaner' in R: |
| install.packages('FastqCleaner', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:FastqCleaner-1.31.0(bioc 3.24)FastqCleaner-1.30.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
qualitycontrolsequencingsoftwaresangerseqsequencematchingcpp
Last updated from:c6bf45ea5d. Checks:12 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 199 | ||
| linux-devel-arm64 | NOTE | 276 | ||
| linux-devel-x86_64 | NOTE | 345 | ||
| source / vignettes | OK | 268 | ||
| linux-release-arm64 | NOTE | 300 | ||
| linux-release-x86_64 | NOTE | 342 | ||
| macos-release-arm64 | NOTE | 224 | ||
| macos-release-x86_64 | NOTE | 391 | ||
| macos-oldrel-arm64 | NOTE | 170 | ||
| macos-oldrel-x86_64 | NOTE | 372 | ||
| windows-devel | NOTE | 329 | ||
| windows-release | NOTE | 340 | ||
| windows-oldrel | NOTE | 301 | ||
| wasm-release | OK | 200 |
Exports:adapter_filtercheck_encodingcomplex_filterfixed_filterinject_letter_randomlaunch_fqclength_filtern_filterqmean_filterrandom_lengthrandom_qualrandom_seqseq_filterseq_namestrim3q_filterunique_filter
Dependencies:abindbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbslibcachemcigarilloclicodetoolscommonmarkcpp11crayoncrosstalkDelayedArraydeldirdigestDTevaluatefastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehighrhtmltoolshtmlwidgetshttpuvhwriterinterpIRangesjpegjquerylibjsonliteknitrlambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeotelpngpromisespwalignR6rappdirsRColorBrewerRcppRcppEigenRhtslibrlangrmarkdownRsamtoolsS4ArraysS4VectorssassSeqinfoshinyshinyBSShortReadsnowsourcetoolsSparseArraySummarizedExperimenttinytexwithrxfunxtableXVectoryaml
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 |
