Man pages for ssarda/genomeutils
Utilities for Genome Analysis
| beta_binom | Bayesian estimation for beta binomial distribution |
| check_inverse | Can the matrix be inverted? |
| color_hclust | Hclust in colour |
| col_scale | Column normalization |
| counts_to_cpm | Compute counts per million (CPM) |
| counts_to_rle | Size Factor normalization as used by DESeq for differential... |
| counts_to_tpm | Convert counts to transcripts per million (TPM). |
| fancy_heatmap | Fancy Heatmap |
| fastload_mat | Load a File as Matrix |
| fastwrite_tab | Write a New File as Tab Delimited |
| fetch_gc_content | Fetch GC content from gene IDs |
| fetch_gene_length | Fetch gene lengths from gene IDs |
| foo_tests | Hypothesis tests |
| GO_analysis | Gene Ontology Analysis |
| GWAS | GWAS |
| logistic.model | Implementing binomial GLM (logistic regression) from scratch. |
| ma_plot | MA plot |
| min_max_scale | Minimum maximum scaling of vector |
| mix.beta | Bayesian estimation for a mixture of betas. |
| mle_gaussian_dist | Gaussian MLE parameters and Model selection |
| mle_weibull_dist | Weibull MLE parameters and Model selection |
| plot_mds | Multi-Dimensional Scaling 2D plot |
| plot_pca | Principal Component Analysis 2D plot |
| plot_svd | Singular Value Decomposition |
| read_genome | Read the genome of a given organism |
| read_proteome | Read the proteome of a given organism |
| row_scale | Row normalization |
| smooth_hist | Smooth Histogram |
| test_lda | Learns and classifies using a Linear Discriminant Analysis... |
| test_limma_lm | Automatic differential gene expression using limma |
| test_nb | Learns and classifies using a Naive Bayes Classifier |
| test_rf | Learns and classifies using a Random Forest Classifier |
| test_svm | Learns and classifies using an SVM |
| uq_scale | Upper Quartile Normalization |
| write_genome | Save a genome in fasta format This function writes to a file.... |
| write_proteome | Save a proteome in fasta format This function writes to a... |
