AIC | AIC |
AIC.comp | Compute and compare AIC for different fasimcoal models |
amplicR | amplicR |
collate.seqs | Collate sequences |
dart2nexus | Convert SNPs data from a genlight object (from Dart... |
data.proc | Data processing |
data.proc.paired | Data processing - paired ends |
deconv | Separate reads by genes and deconvolute them based on... |
detect | Detect a reference sequence |
fsc.bootstraps | Compute bootstrap confidence intervals for estimated... |
fsc.estimate | Run fastsimcoal to estimate parameters' values |
fsc.multiple.estimate | Run fsc over multiple models |
getnFiltered | Return the number of filtered sequences from a derep obj |
getnUniques | Return the number of unique sequences in a derep obj |
getRow | Extracts rows from a matrix into a vector |
getSeqFromDerep | Extract sequences from a derep object |
gl2sfs | Convert a genlight object into a sfs input file |
make.alleles | Build (possible) allele sequences based on genotypes |
make.phyloseq | Create a phyloseq object |
ndada | Return the number of unique sequences in a dada obj |
putna | Replace null values with NA |
putzero | Replace null values with zero or x with x - 1 |
raw2data.proc | From raw data to data.proc() |
replaceSNP | Replace SNPs with IUPAC ambiguities |
rmEndAdapter | Remove end adapter |
sel.match | Select appropriate hits when searching a patter |
setup | Set up environment to use 'amplicR' |
subsetDerep | Subset a derep-class based on abundance of the reads |
table2fasta | Write unique sequences to a fasta file for each sample where... |
where2trim | Select position where a pattern has been found |
write.nexus | Write a nexus file from a DNAStringSet object |
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