Commit 70258e49 authored by Etienne Rifa's avatar Etienne Rifa
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license + resolve warnings + conflicts

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^ranomaly\.Rproj$
^\.Rproj\.user$
^LICENSE\.md$
Package: ranomaly
Title: An R package grouping ANOMALY worflow functions.
Version: 0.0.0.9000
Authors@R: c(
person(family = "Theil", given = "Sebastien", email = "sebastien.theil@inrae.fr", role = c("aut", "cre")),
person(family = "Rifa", given = "Etienne", email = "etienne.rifa@inrae.fr", role = c("aut"))
)
Description: rANOMALY use Amplicon Sequence Variant (ASV from Dada2 package) as taxonomic unit, allowing an easy and relevant sequence tracking between different environments and/or projects.
Decontam package is included for an accurate and consistent detection of contaminant ASV and taxonomic assignment step relies on IDTAXA method. Our workflow is able to merge and check
annotations from two taxonomic databases to unravel misannotation, discordance or inconsistency. The well known Phyloseq package provides the most common graphical representation,
with additional statistics to assess significant impact of tested factors on microbial communities. The workflow incorporate multiple differential analyses (DESeq2 etc...)
to reveal thin community contrast between conditions.
License: GPL 3.0
Authors@R:
c(person(given = "Sebastien",
family = "Theil",
role = c("aut", "cre"),
email = "sebastien.theil@inrae.fr"),
person(given = "Etienne",
family = "Rifa",
role = "aut",
email = "etienne.rifa@inrae.fr"))
Description: rANOMALY use Amplicon Sequence Variant (ASV from Dada2
package) as taxonomic unit, allowing an easy and relevant sequence
tracking between different environments and/or projects. Decontam
package is included for an accurate and consistent detection of
contaminant ASV and taxonomic assignment step relies on IDTAXA method.
Our workflow is able to merge and check annotations from two taxonomic
databases to unravel misannotation, discordance or inconsistency. The
well known Phyloseq package provides the most common graphical
representation, with additional statistics to assess significant
impact of tested factors on microbial communities. The workflow
incorporate multiple differential analyses (DESeq2 etc...) to reveal
thin community contrast between conditions.
License: GPL (>= 3)
Depends:
R (>= 3.6)
Imports:
Biobase,
BiocGenerics,
Biostrings,
dada2,
DECIPHER,
decontam,
DESeq2,
digest,
doParallel,
dplyr,
foreach,
futile.logger,
ggplot2,
ggpubr,
glue,
grid,
gridExtra,
gtools,
htmlwidgets,
IRanges,
metacoder,
metagenomeSeq,
microbiome,
mixOmics,
nlme,
pairwiseAdonis,
phangorn,
phyloseq,
plotly,
psadd,
ranacapa,
reshape2,
scales,
ShortRead,
tools,
utils,
vegan,
venn,
VennDiagram
Remotes:
bioc::3.10/Biostrings,
bioc::3.10/dada2,
bioc::3.10/DECIPHER,
bioc::3.10/decontam,
bioc::3.10/metagenomeSeq,
bioc::3.10/microbiome,
bioc::3.10/mixOmics,
bioc::3.10/phyloseq,
bioc::3.10/ShortRead,
github::cpauvert/psadd,
github::gauravsk/ranacapa,
github::grunwaldlab/metacoder,
github::mikelove/DESeq2,
github::mixOmicsTeam/mixOmics,
github::pmartinezarbizu/pairwiseAdonis/pairwiseAdonis
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports:
backports,
XML,
vctrs,
biomformat,
Biostrings,
Biobase,
BiocGenerics,
gtools,
ShortRead,
dada2,
decontam,
dplyr,
microbiome,
DESeq2,
metagenomeSeq,
metacoder,
ggpubr,
pairwiseAdonis,
phyloseq,
psadd,
VennDiagram,
digest,
futile.logger,
ggplot2,
glue,
grid,
gridExtra,
vegan,
viridis,
nlme,
phangorn,
plotly,
taxa,
rmarkdown,
ranacapa,
reshape2,
doParallel,
foreach,
DECIPHER,
mixOmics,
venn,
htmlwidgets,
scales
Remotes:
github::omegahat/XML,
bioc::3.10/biomformat,
bioc::3.10/Biostrings,
bioc::3.10/ShortRead,
bioc::3.10/dada2,
bioc::3.10/decontam,
bioc::3.10/metagenomeSeq,
bioc::3.10/phyloseq,
bioc::3.10/microbiome,
bioc::3.10/DECIPHER,
bioc::3.10/mixOmics,
github::pmartinezarbizu/pairwiseAdonis/pairwiseAdonis,
github::cpauvert/psadd,
github::gauravsk/ranacapa,
github::grunwaldlab/metacoder,
github::mixOmicsTeam/mixOmics,
github::mikelove/DESeq2
This diff is collapsed.
......@@ -53,7 +53,6 @@ import(plotly)
import(psadd)
import(reshape2)
import(scales)
import(stringr)
import(vegan)
importFrom(Biobase,AnnotatedDataFrame)
importFrom(Biobase,fData)
......@@ -80,8 +79,10 @@ importFrom(metacoder,calc_obs_props)
importFrom(metacoder,calc_taxon_abund)
importFrom(metacoder,compare_groups)
importFrom(metacoder,diverging_palette)
importFrom(metacoder,filter_obs)
importFrom(metacoder,heat_tree)
importFrom(metacoder,parse_phyloseq)
importFrom(metacoder,taxon_names)
importFrom(metacoder,zero_low_counts)
importFrom(microbiome,aggregate_top_taxa)
importFrom(microbiome,core_members)
......@@ -94,6 +95,4 @@ importFrom(phangorn,pml)
importFrom(plotly,ggplotly)
importFrom(ranacapa,ggrare)
importFrom(reshape2,melt)
importFrom(taxa,filter_obs)
importFrom(taxa,taxon_names)
importFrom(venn,venn)
......@@ -14,7 +14,6 @@
#' @param compress Reads files are compressed (.gz)
#' @param verbose Verbose level. (1: quiet, 3: verbal)
#' @param torrent_single Boolean to choose between Illumina Paired End SOP or Torrent Single End SOP. default: FALSE
#' @param torrent_trim Sequence length to trim at 3' and 5' for single end torrent data. (0 = no trim)
#' @param trim_l Trim left size.
#' @param trim_r Trim right size.
#' @param returnval Boolean to return values in console or not.
......@@ -31,7 +30,6 @@
#' @import futile.logger
#' @import digest
#' @import phyloseq
#' @import stringr
#' @export
# DADA2 function
......@@ -52,7 +50,7 @@ dada2_fun <- function(amplicon = "16S", path = "", outpath = "./dada2_out/", f_t
flog.info("Creating directory.")
if(!dir.exists(outpath)){
dir.create(outpath)
dir.create(outpath, recursive = TRUE)
}
flog.info('Done.')
......
......@@ -10,7 +10,7 @@
#' @param plot1 Plot heattrees or not
#' @param signif Plot only siignificant or not
#'
#' @importFrom metacoder calc_obs_props
#' @importFrom metacoder calc_obs_props filter_obs
launch_metacoder <- function(psobj, min, col, rank, title = "", plot1 = TRUE, signif = TRUE){
......@@ -207,15 +207,7 @@ launch_metacoder <- function(psobj, min, col, rank, title = "", plot1 = TRUE, si
#'
#' @import phyloseq
#' @import ggplot2
#' @importFrom metacoder zero_low_counts
#' @importFrom metacoder calc_taxon_abund
#' @importFrom metacoder calc_n_samples
#' @importFrom metacoder compare_groups
#' @importFrom metacoder parse_phyloseq
#' @importFrom metacoder heat_tree
#' @importFrom metacoder diverging_palette
#' @importFrom taxa filter_obs
#' @importFrom taxa taxon_names
#' @importFrom metacoder zero_low_counts calc_taxon_abund calc_n_samples compare_groups parse_phyloseq heat_tree diverging_palette taxon_names
#' @importFrom gridExtra marrangeGrob
#'
#' @export
......
......@@ -3,7 +3,8 @@
#' Allows subset fastq or fasta files at a given threshold. This function can convert fastq to fasta.
#'
#' @param path Path to the fastq files directory
#' @param format fasta or fastq format are allowed.
#' @param format input format, fasta or fastq format are allowed.
#' @param outformat output format, fasta or fastq format are allowed.
#' @param output Path to the output directory
#' @param nbseq Number of sequences to output per fastq files; if NULL no subset.
#' @param ncores Number of CPU used to process.
......
......@@ -58,8 +58,6 @@ dada2_fun(
\item{trim_r}{Trim right size.}
\item{orient_torrent}{Forward primer sequence to orient all reads to same strand.}
\item{torrent_trim}{Sequence length to trim at 3' and 5' for single end torrent data. (0 = no trim)}
}
\value{
Return raw otu table in phyloseq object and export it in an Rdata file.
......
......@@ -20,7 +20,9 @@ subset_fastx(
\arguments{
\item{path}{Path to the fastq files directory}
\item{format}{fasta or fastq format are allowed.}
\item{format}{input format, fasta or fastq format are allowed.}
\item{outformat}{output format, fasta or fastq format are allowed.}
\item{output}{Path to the output directory}
......
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