Man pages for ssarda/genomeutils
Utilities for Genome Analysis

beta_binomBayesian estimation for beta binomial distribution
check_inverseCan the matrix be inverted?
color_hclustHclust in colour
col_scaleColumn normalization
counts_to_cpmCompute counts per million (CPM)
counts_to_rleSize Factor normalization as used by DESeq for differential...
counts_to_tpmConvert counts to transcripts per million (TPM).
fancy_heatmapFancy Heatmap
fastload_matLoad a File as Matrix
fastwrite_tabWrite a New File as Tab Delimited
fetch_gc_contentFetch GC content from gene IDs
fetch_gene_lengthFetch gene lengths from gene IDs
foo_testsHypothesis tests
GO_analysisGene Ontology Analysis
GWASGWAS
logistic.modelImplementing binomial GLM (logistic regression) from scratch.
ma_plotMA plot
min_max_scaleMinimum maximum scaling of vector
mix.betaBayesian estimation for a mixture of betas.
mle_gaussian_distGaussian MLE parameters and Model selection
mle_weibull_distWeibull MLE parameters and Model selection
plot_mdsMulti-Dimensional Scaling 2D plot
plot_pcaPrincipal Component Analysis 2D plot
plot_svdSingular Value Decomposition
read_genomeRead the genome of a given organism
read_proteomeRead the proteome of a given organism
row_scaleRow normalization
smooth_histSmooth Histogram
test_ldaLearns and classifies using a Linear Discriminant Analysis...
test_limma_lmAutomatic differential gene expression using limma
test_nbLearns and classifies using a Naive Bayes Classifier
test_rfLearns and classifies using a Random Forest Classifier
test_svmLearns and classifies using an SVM
uq_scaleUpper Quartile Normalization
write_genomeSave a genome in fasta format This function writes to a file....
write_proteomeSave a proteome in fasta format This function writes to a...
ssarda/genomeutils documentation built on May 30, 2019, 8:42 a.m.