Man pages for caseywdunn/agalmar
A Collection of Tools for Analyzing Agalma Expression Projects
| agalmar | agalmar: A Collection of Tools for Analyzing Agalma... |
| apply_normalizations | Takes a DGEList object, and returns a matrix of normalized... |
| create_DESeq2 | Creates a DESeqDataSet object |
| create_DESeq2-Expression-formula-method | Creates a DESeqDataSet object |
| dataframe_to_node_labels | Converts data frame of node annotations to NHX node labels |
| decompose_orthologs | Decomposes a gene tree into a list of subtrees that have no... |
| DGEList-class | "DGEList" class |
| Expression | Construct an Expression object from list of experiment data... |
| Expression-class | An S4 class to represent gene expression data for multiple... |
| get_lane | Get lane from Illumina fastq sequence header |
| get_run | Get run from Illumina fastq sequence header |
| get_tip_info | Parse species and sequence id from a phy |
| has_species | Returns true if all species are in the tree tips |
| janedoe | Expression data for different tissues from an animal |
| nhx_label_to_list | Converts a NHX node label string to a list of named values |
| node_support | Parse support from node name |
| parse_gene_tree | Parses text to a gene tree |
| plot_matrix | Plots a matrix |
| species | Get species |
| species-Expression-method | Get the species |
| summarize_edges | Create a data frame with summary statistics for edges in a... |
| summarize_libraries | Summarize expression libraries |
| summarize_libraries-Expression-method | Summarize expression libraries |
| summarize_nodes | Create a data frame with summary statistics for nodes in a... |
| summarize_reference | Summarize reference sequences |
| summarize_reference-Expression-method | Summarize reference sequences |
| summary_libraries | Create a data frame with summary statistics for expression... |
| summary_references | Create a data frame with summary statistics for reference... |
