Man pages for SchwartzLab/brainSTORM
brainSTORM. A package to process STORM-seq based data
| ac4C_scores | ac4C scores |
| add_2OmeScore | Add 2-O-methylation score to STORM-seq object |
| add_CtoT_MRD | Add C-to-T misincorporation difference |
| add_CytPer | Add cytidine persistance index to STORM object |
| add_default_metrics_v1 | Add all default metrics for STORMseq v1 |
| add_default_metrics_v2 | Add all default metrics for STORMseq v2 |
| add_DR | Add deletion rate |
| add_DRD | Add deletion rate difference |
| add_ER | Add read-end to coverage ratio |
| add_ER1bpDS | Add end rate 1bp downstream |
| add_ERlog2FCh | Add End ratio log2-Fold-Change |
| add_ERlog2FCh1bpDS | Add End ratio log2-Fold-Change 1bp downstream |
| addKnownRNAmods | Add known RNA modifications nucleotide identity |
| add_MR | Add Misincorporation Rate |
| add_MRD | Add Misincorporation Rate Difference |
| add_scoreA3p | Add ScoreA accounting for read-ends (3prime) |
| add_scoreA5p | Add ScoreA accounting for read-starts (5prime) |
| add_scoreC3p | Add ScoreC accounting for read-stops (3prime) |
| add_scoreZ_3p | Add scoreZ accounting for read-ends (3prime) |
| add_SR | Add Read-start to coverage ratio |
| add_SR1bpDS | Add read-start to coverage rate 1 bp down-stream |
| add_SRD | Add Start Ratio Difference |
| add_SRD1bpDS | Add Start Ratio Difference 1bp down-stream |
| add_SRlog2FCh1bpDS | Add Start ratio log2-Fold-Change 1bp down-stream |
| alignSTAR | STAR alignment |
| bam2TxDT | BAM to txDataTable |
| bisGenome | Make bisulphite genome |
| brainSTORM-package | brainSTORM: brainSTORM. A package to process STORM-seq based... |
| call_RNAmods_logRegMods | Logistic regressions scores |
| fastq_nucFreq | Nucleotide frequency report |
| gg_lce | Library complexity extrapolation plot |
| gg_nucFreq | nucleotide frequency plot |
| gg_readStats | Alignment report plots |
| hlp_assign_scores | Assign scores to respective RNAmods in STORM$CALLS |
| hlp_start_CALLS | Initialize STORM$CALLS |
| libComplexReport | Library complexity report |
| m1A_scores | m1A scores |
| m3U_scores | m3U scores |
| m5C_scores | m5C scores |
| m7G_scores | m7G scores |
| mkBedFromFastaTxOme | Make BED from FASTA Transcriptome |
| mkSTARgenome | Make STAR genome |
| mkTranscriptome | Make transcriptome |
| Nm_scores | 2-O-methylation scores |
| reads_report | Alignment report table |
| rmTmpDir | Remove STORM temporary directory |
| RNAmods_vec | STORM base coordinate columns |
| rRNAmods_Sc_Taoka | Yeast rRNA modifications reference |
| storm_assignScores | Assigning default Scores to tables by sets of samples |
| storm_baseCols | STORM base columns |
| storm_baseCoorCols | STORM base coordinate columns |
| storm_evalPreds | Evaluate predictions |
| storm_META | Create STORM META - Experiment design matrix |
| storm_metricsBoxPlot_byNuc | Boxplots of $RES calculated metrics grouping by modified... |
| storm_metricsScatterPlot_byPos | STORM scatterplot of scores by txcoor |
| storm_plot_confMat | Confussion matrix plot |
| storm_STORM | STORM object constructor from META table |
| yeast_STORM | Yeast STORM object |
| Y_scores | Pseudouridine scores |
