Man pages for timjeske/DEUS
Differential expression of unique sequences
| addCountsOfFeatureClasses | Count occurrences of feature classes |
| createCountTableFromFastQs | Create sequence-based count tables |
| createMap | Create a mapping of sequences to sequence identifiers |
| deleteTmp | Remove temporary FASTA file required for clustering |
| getConditionCountStats | Compute mean and standard deviation of normalized counts for... |
| getNoBlastHitFraction | Compute fraction of reads without BLAST hit for each sample |
| mergeAndAggregate | Aggregates sequence counts for each sequence cluster |
| mergeResults | Merge intermediate results of DEUS |
| mergeSingleAndClusterResults | Merges clustering results as well as DE results for single... |
| plotPCA | Plot result of PCA |
| plotSampleDistanceMap | Plot sample distance heatmap |
| printCluster | Print FASTA file for cluster of sequences |
| printClusterSummary | Prints a summary of the number of significant sequences and... |
| processClusters | Processes CD-HIT result file |
| runBlast | Run BLAST for small RNA sequences |
| runClustering | Run CD-HIT clustering |
| runDESeq2 | Run differential expression analysis based on DESeq2 |
| sequencesAsFasta | Create a vector of sequence identifiers and sequences in... |
| writeSummaryFiles | Write summary tables for DEUS result |
