Man pages for hallucigenia-sparsa/seqgroup
Analysis of Sequencing Data with Groups
| aggregateTaxa | Aggregate a taxon abundance matrix |
| assignColorsToGroups | Assign colors to groups |
| assignMetadataTypes | Assign data types to metadata |
| barebonesCoNet | Barebones R implementation of CoNet |
| buildNetwork | Build a microbial network |
| clr | Centered log-ratio (CLR) transform |
| compareDistribs | Compare the distribution of a taxon across two groups |
| compareGroups | Compare diversity-related properties across groups |
| exportToCoNet | Export taxon abundances in a format suitable for CoNet |
| filterMetadata | Filter metadata |
| filterTaxonMatrix | Filter taxa in an abundance matrix |
| findClusters | Cluster taxon- or sample-wise |
| floresgut_lineages | Lineages for gut taxa from Flores et al. |
| floresgut_metadata | Gut sample metadata from Flores et al. |
| floresgut_taxa | Gut taxon abundances from Flores et al. |
| getCoreTaxa | List core taxa across groups |
| groupBarplot | Bar plot of taxon composition with group support |
| ibd_functions | Functions from the PRISM cohort |
| ibd_lineages | Lineages for taxa from the PRISM cohort |
| ibd_metadata | Metadata for the PRISM cohort |
| ibd_taxa | IBD and control taxon abundances from the PRISM cohort |
| intersectTables | Table intersection |
| makeColorsGivenMetadata | Assign colors such that they encode a metadata item |
| mergeATC | Merge ATC codes |
| mergeTables | Table union |
| metadataToNumeric | Convert metadata into numeric form |
| networkIntersectSig | Significance of network intersection |
| normalize | Normalize a matrix |
| removeGroupsWithMissingValues | Remove groups that have metadata items with missing values |
| selectGroups | Select groups |
| selectSamplesGivenMetadata | Split samples into groups given metadata. |
| seqgroup | Analysis of Sequencing Data with Groups |
| seqPCoA | PCoA for microbial sequencing data |
| setNAToGroupMean | Replace missing values by group mean. |
| silhouette | Get silhouette score for a clustering result |
| sortSamples | Sort samples by group and optionally by time. |
| toPhyloseq | Convert abundances to phyloseq object |
| transitionProbabs | Compute transition probabilities between clusters |
