Man pages for pmartR/pmartRseq
Analysis and Visualization of 16S Data
| abundance_calc | Calculates Abundance |
| alphaDiv_calc | Calculates Alpha Diversity Indices |
| applyFilt | Apply a filter to an omicsData object |
| applyFilt_worker | Remove items that need to be filtered out |
| as.seqData | Convert Data to Appropriate pmartRseq Class |
| CLR_Norm | Centered-log Ratio Normalization of count data |
| count_based_filter | Count filter object |
| countSTAT | Statistical tests for count data |
| CSS_Norm | Cumulative sum scaling normalization of count data |
| detect_modules | Detect modules for Network |
| effsp_calc | Calculates Effective Species |
| evenness_calc | Calculates Evenness Indices |
| group_designation | Creates Data Frame for Group Membership Based on Specified... |
| import_seqData | Import rRNA (16S/ITS/18S), metatranscript, or metagenomic... |
| indsp_calc | Computes Indicator Species Analysis for Count Data |
| jaccard_calc | Calculates Jaccard Index |
| Log_Norm | Log transformation of count data |
| med_scounts_norm | Normalization of count data via DESeq scale factors |
| metadata_based_filter | Metadata filter object |
| mod_env | Function to calculate module eigen vectors and correlate... |
| network_calc | Calculates Correlations |
| network_indices | Calculate Indices (metrics) for Network |
| network_plot | Generate Network Plot |
| normalize_data | Normalize data |
| plot_all_diffabun | Plot all differential abundance results |
| plot_indsp | Plot Indicator species Analysis Results |
| plot_pmartRseq | Produce a plot of an omicsData Object |
| pmartRseq | pmartRseq: A pipeline package that enables a reproducible... |
| pmartRseq_aldex2 | Modified version of ALDEx2 for pmartRseq |
| pmartRseq_DESeq2 | DESeq2 analysis of omicsData objects |
| pmartRseq_edgeR | edgeR analysis of omicsData objects |
| pmartRseq_igraph | Calculates a network graph |
| pmartRseq_NMDS | NMDS plot for beta diversity |
| pmartRseq_to_vegan | Transforms an omicsData object into a vegan data object |
| poisson_norm | Normalization of count data via Poisson Sampling |
| Quant_Norm | Quantile normalization of count data |
| Rarefy | Rarefying of count data |
| report | Creates a report for pmartRseq objects |
| richness_calc | Calculates Richness |
| sample_based_filter | Sample filter object |
| split_emeta | Splits an e_meta column into separate columns |
| summary-pmartRseq | Produce a basic summary of an pmartRseq S3 Object |
| taxa_rollup | Roll up data to a specified taxonomic level |
| TMM_Norm | Trimmed Mean of M Values normalization of count data |
| TSS_Norm | Total sum scaling normalization of count data |
