Man pages for caseywdunn/agalmar
A Collection of Tools for Analyzing Agalma Expression Projects

agalmaragalmar: A Collection of Tools for Analyzing Agalma...
apply_normalizationsTakes a DGEList object, and returns a matrix of normalized...
create_DESeq2Creates a DESeqDataSet object
create_DESeq2-Expression-formula-methodCreates a DESeqDataSet object
dataframe_to_node_labelsConverts data frame of node annotations to NHX node labels
decompose_orthologsDecomposes a gene tree into a list of subtrees that have no...
DGEList-class"DGEList" class
ExpressionConstruct an Expression object from list of experiment data...
Expression-classAn S4 class to represent gene expression data for multiple...
get_laneGet lane from Illumina fastq sequence header
get_runGet run from Illumina fastq sequence header
get_tip_infoParse species and sequence id from a phy
has_speciesReturns true if all species are in the tree tips
janedoeExpression data for different tissues from an animal
nhx_label_to_listConverts a NHX node label string to a list of named values
node_supportParse support from node name
parse_gene_treeParses text to a gene tree
plot_matrixPlots a matrix
speciesGet species
species-Expression-methodGet the species
summarize_edgesCreate a data frame with summary statistics for edges in a...
summarize_librariesSummarize expression libraries
summarize_libraries-Expression-methodSummarize expression libraries
summarize_nodesCreate a data frame with summary statistics for nodes in a...
summarize_referenceSummarize reference sequences
summarize_reference-Expression-methodSummarize reference sequences
summary_librariesCreate a data frame with summary statistics for expression...
summary_referencesCreate a data frame with summary statistics for reference...
caseywdunn/agalmar documentation built on Aug. 5, 2018, 9:10 p.m.