Package: tidyGenR 0.1.8

tidyGenR: Tidy Multilocus Amplicon Genotypes

Variant determination and genotyping from high throughput sequences from multilocus amplicon libraries, typically sequenced in Illumina MiSeq or similar. It provides a set of core functions for the central steps: demultiplex by locus, truncate reads, variant calling, and genotype calling. Additionally, it provides a set of functions for diagnosis and estimation of best running parameters and multiple extensions for genotype/variants manipulation and reformatting. Output variants and genotypes are output in 'tidy' format, thus facilitating reformatting, manipulation and potential connection to other R packages.

Authors:Miguel Camacho [aut, cre, cph], Jennifer Leonard [fnd]

tidyGenR_0.1.8.tar.gz
tidyGenR_0.1.8.zip(r-4.7-any)tidyGenR_0.1.8.zip(r-4.6-any)tidyGenR_0.1.8.zip(r-4.5-any)
tidyGenR_0.1.8.tgz(r-4.6-any)tidyGenR_0.1.8.tgz(r-4.5-any)
tidyGenR_0.1.8.tar.gz(r-4.7-any)tidyGenR_0.1.8.tar.gz(r-4.6-any)
tidyGenR_0.1.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tidyGenR/json (API)

# Install 'tidyGenR' in R:
install.packages('tidyGenR', repos = c('https://csmiguel.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/csmiguel/tidygenr/issues

Datasets:

On CRAN:

Conda:

softwaresequencingclassificationphylogenetics

4.86 score 1 stars 12 scripts 194 downloads 26 exports 89 dependencies

Last updated from:c8f9e1eae7. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE396
source / vignettesOK317
linux-release-x86_64NOTE398
macos-release-arm64NOTE290
macos-oldrel-arm64NOTE275
windows-develNOTE352
windows-releaseNOTE373
windows-oldrelNOTE294
wasm-releaseOK171

Exports:align_variants_refamplisas2tidycheck_raw_readscompare_callsdemultiplexdereplicateexplore_dadafilter_variantsgen_compact2widegen_tidy2compactgen_tidy2genalexgen_tidy2integersgen_tidy2widegen_wide2structuregenotypeout_popartreads_loci_samplesreads_trackremove_hemizygotesremove_monomorphicremove_poor_fastqrename_allelestidy2sequencestrunc_ampvar_seq2lenvariant_call

Dependencies:abindBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopscigarilloclicliprcodetoolscpp11crayondada2DBIDECIPHERDelayedArraydeldirdigestdplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehmshwriterinterpIRangesisobandjpeglabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatspatchworkpillarpkgconfigplyrpngprettyunitsprogresspurrrpwalignR6RColorBrewerRcppRcppEigenRcppParallelreadrreshape2RhtslibrlangRsamtoolsS4ArraysS4VectorsS7scalesSeqinfoShortReadsnowSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrwritexlXVector

Introduction to tidyGenR
Introduction | Input raw sequences | Demultiplex loci | Truncate reads | Variant calling | Genotype
Rendered fromtidyGenR-intro.Rmdusingknitr::rmarkdown

Last update: 2026-02-13
Started: 2025-04-06

Optimization of variant calling
Introduction | explore_dada() | compare_calls()
Rendered fromtidyGenR-optimization.Rmdusingknitr::rmarkdown

Last update: 2026-02-09
Started: 2026-02-09

Readme and manuals

Help Manual

Help pageTopics
add allele_no to genotypesadd_allele_no
Align variant sequences against a reference FASTA databasealign_variants_ref
Read AmpliSAT results into tidy variantsamplisas2tidy
Check input raw FASTA/Q filescheck_raw_reads
Check1check1_lowcount
Check2check2_unique_snames
Check3check3_non_orphan
Comparision between multiple tidy variants or genotypes.compare_calls
Create cutadapt commandcutadapt_command
Demultiplex reads by locusdemultiplex
De-replicate reads into frequency tables for a set of FASTQ filesdereplicate
Distance between two matricesdist_m
Applies distance between all tables in a list.dist_m_all
Explore variants output by DADA2 in the parameter spaceexplore_dada
Filter variants based on frequency and depthfilter_variants
Genotype samples from tidy variantsgenotype geno_direct
Conversion among genotype formats: tidy, compact, wide, STRUCTUREgenotype_conversion gen_compact2wide gen_tidy2compact gen_tidy2genalex gen_tidy2integers gen_tidy2wide gen_wide2structure
Genotypesgenotypes
plot MDSmds_comp
Format MSA and traits for PopArtout_popart
Primers for multiplex PCRprimers
Output reads per locusreads_loci_samples
Output reads across pipelinereads_track
Remove hemizygote callsremove_hemizygotes
Remove monorphic lociremove_monomorphic
Remove empty FASTQremove_poor_fastq
Rename alleles in a dataframe based on reference allelesrename_alleles
Remove Ns introduced in 'mergePairs(justConcatenate = T)'rm_n_msa
Output FASTA sequencestidy2sequences
Per-locus truncation lengths for forward and reverse reads.trunc_fr
Truncate readstruncate trunc_amp
Convert sequence-based variants to length-basedvar_seq2len
Variant callingvariant_call
Variant calling using DADA2 ASV approachchimera_removal dada2list loess_err_mod4 variant_calling_dada variant_call_dada
List of tidy variantsvariant_calls
Variantsvariants