Man pages for mworkentine/mattsUtils
Personal Utility Functions For Various Analysis

add_taxonomy_columnAdd taxonomy label
cluster_orderCluster Order
compute_spiacompute spia with provided gene list does the bulk of the...
get_monophyletic_subsetsGet monophyletic subsets
get_richnessGet a dataframe with richness estimates
get_seq_statsSequence stats
get_sig_taxaGet a list of significant taxa from a DESeq analysis
ggheatmapMake a ggplot heatmap
lfc_plotLog fold-change plot
make_heatmapMake Heatmap
make_ordination_plotsMake ordination plots
make_prev_dfMake a prevalance dataframe
make_taxa_coloursMake colour palettes for taxa
mattsUtilsmattsUtils: Convience functions and utilies to help with my...
plot_bar2Plot bar 2
plot_diagnositicsDiagnostic plots for a DESeq differential expression analysis
plot_featureCount_statsPlot stats from featureCounts output
plot_genus_by_phylumPlot genus by phylum
plot_num_seqsPlot number of sequences
plot_OTUsPlot OTUs
plotPCA2Plot PCA (modified)
prev_filtPrevalance filter
prev_plotPrevelance Plot
print_tablePrint table
psmelt_dplyrA dplyr version of psmelt
replace_countsReplace counts
rlog_norm_otusrlog normalize an OTU table
run_spiaPrepare gene lists and run spia
single_gene_plotSingle Gene Plot
subset_samples_safeSubset samples 2
subset_taxa_safeSubset taxa 2
summarize_taxonomySummarize taxonomy
tidy_phyloseqTidy phyloseq
upload_and_shareUpload and share
veganotuConvert phyloseq otu table to vegan otu table
vst_transformVST Tranform a phyloseq object
mworkentine/mattsUtils documentation built on May 23, 2019, 11:58 a.m.