Package: Anaconda 0.1.5

Anaconda: Targeted Differential and Global Enrichment Analysis of Taxonomic Rank by Shared Asvs

Targeted differential and global enrichment analysis of taxonomic rank by shared ASVs (Amplicon Sequence Variant), for high-throughput eDNA sequencing of fungi, bacteria, and metazoan. Actually works in two steps: I) Targeted differential analysis from QIIME2 data and II) Global analysis by Taxon Mann-Whitney U test analysis from targeted analysis (I) (I) Estimate variance-mean dependence in count/abundance ASVs data from high-throughput sequencing assays and test for differential represented ASVs based on a model using the negative binomial distribution. (II) NCBITaxon_MWU uses continuous measure of significance (such as fold-change or -log(p-value)) to identify NCBITaxon that are significantly enriches with either up- or down-represented ASVs. If the measure is binary (0 or 1) the script will perform a typical 'NCBITaxon enrichment' analysis based Fisher's exact test: it will show NCBITaxon over-represented among the ASVs that have 1 as their measure. On the plot, different fonts are used to indicate significance and color indicates enrichment with either up (red) or down (blue) regulated ASVs. No colors are shown for binary measure analysis. The tree on the plot is hierarchical clustering of NCBITaxon based on shared ASVs. Categories with no branch length between them are subsets of each other. The fraction next to the category name indicates the fraction of 'good' ASVs in it; 'good' ASVs are the ones exceeding the arbitrary absValue cutoff (option in taxon_mwuPlot()). For Fisher's based test, specify absValue=0.5. This value does not affect statistics and is used for plotting only. The original idea was for genes differential expression analysis from Wright et al (2015) <doi:10.1186/s12864-015-1540-2>; adapted here for taxonomic analysis. The 'Anaconda' package makes it possible to carry out these analyses by automatically creating several graphs and tables and storing them in specially created subfolders. You will need your QIIME2 pipeline output for each kingdom (eg; Fungi and/or Bacteria and/or Metazoan): i) taxonomy.tsv, ii) taxonomy_RepSeq.tsv, iii) ASV.tsv and iv) SampleSheet_comparison.txt (the latter being created by you).

Authors:Pierre-Louis Stenger [cre, aut]

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Anaconda.pdf |Anaconda.html
Anaconda/json (API)

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

Peer review:

Bug tracker:https://github.com/plstenger/anaconda/issues

On CRAN:

2.70 score 475 downloads 38 exports 75 dependencies

Last updated 6 months agofrom:75f263c08a. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winWARNINGNov 05 2024
R-4.5-linuxWARNINGNov 05 2024
R-4.4-winWARNINGNov 05 2024
R-4.4-macWARNINGNov 05 2024
R-4.3-winWARNINGNov 05 2024
R-4.3-macWARNINGNov 05 2024

Exports:BacteriaclusteringGOsdasva_raw_inputdatabase_bacteria_creationdatabase_fungi_creationdatabase_fungi_creation_RepSeqdatabase_metazoan_creationfisherTestformat_inputFungifunguild_input_targetedget_bactotraits_targetedget_dasvaget_funguildsget_funguilds_targetedget_input_filesget_link_guildsget_taxon_list_drawerheatmap_conditionheatmap_data_dasvaheatmap_samples_hclustheatmap_samples_matrixheatmap_taxoinput_global_analysisMetazoanmove_filesmwuTestPCA_data_dasvaplotDispASVsplotMA.dasvaplotPCA.sanplotSparsityASVsamplesInfotarget_filetaxon_mwu_listtaxon_mwuPlottaxon_mwuPlot_guildstaxon_mwuStats

Dependencies:abindapeaskpassBHBiobaseBiocGenericsBiocParallelclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayDESeq2digestfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelocfitlookupmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigplyrR6rafalibRColorBrewerRcppRcppArmadillorlangS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
BacteriaBacteria
clusteringGOsclusteringGOs
dasva_raw_inputdasva_raw_input
database_bacteria_creationdatabase_bacteria_creation
database_fungi_creationdatabase_fungi_creation
database_fungi_creation_RepSeqdatabase_fungi_creation_RepSeq
database_metazoan_creationdatabase_metazoan_creation
fisherTestfisherTest
format_inputformat_input
FungiFungi
funguild_input_targetedfunguild_input_targeted
get_bactotraits_targetedget_bactotraits_targeted
get_dasvaget_dasva
get_funguildsget_funguilds
get_funguilds_targetedget_funguilds_targeted
get_input_filesget_input_files
get_link_guildsget_link_guilds
get_taxon_list_drawerget_taxon_list_drawer
heatmap_conditionheatmap_condition
heatmap_data_dasvaheatmap_data_dasva
heatmap_samples_hclustheatmap_samples_hclust
heatmap_samples_matrixheatmap_samples_matrix
heatmap_taxoheatmap_taxo
input_global_analysisinput_global_analysis
MetazoanMetazoan
move_filesmove_files
mwuTestmwuTest
PCA_data_dasvaPCA_data_dasva
plotDispASVsplotDispASVs
plotMA.dasvaplotMA.dasva
plotPCA.sanplotPCA.san
plotSparsityASVplotSparsityASV
samplesInfosamplesInfo
target_filetarget_file
taxon_mwu_listtaxon_mwu_list
taxon_mwuPlottaxon_mwuPlot
taxon_mwuPlot_guildstaxon_mwuPlot_guilds
taxon_mwuStatstaxon_mwuStats