API for SchwartzLab/brainSTORM
brainSTORM. A package to process STORM-seq based data
| Global functions | |
|---|---|
| CV_balancedGroups | Source code |
| MCC | Source code |
| Nm_scores | Man page |
| RNAmods_vec | Man page |
| Y_scores | Man page |
| ac4C_scores | Man page |
| addKnownRNAmods | Man page |
| add_2OmeScore | Man page Source code |
| add_CtoT_MRD | Man page Source code |
| add_CytPer | Man page Source code |
| add_DR | Man page Source code |
| add_DRD | Man page Source code |
| add_ER | Man page Source code |
| add_ER1bpDS | Man page Source code |
| add_ERlog2FCh | Man page Source code |
| add_ERlog2FCh1bpDS | Man page Source code |
| add_EndRate | Source code |
| add_EndRate1bpDS | Source code |
| add_MR | Man page Source code |
| add_MRD | Man page Source code |
| add_Nm_MgR_metrics | Source code |
| add_Nm_metrics | Source code |
| add_SR | Man page Source code |
| add_SR1bpDS | Man page Source code |
| add_SRD | Man page Source code |
| add_SRD1bpDS | Man page Source code |
| add_SRlog2FCh1bpDS | Man page Source code |
| add_StartRate | Source code Source code |
| add_StartRate_1bpDS | Source code |
| add_Y_metrics | Source code |
| add_ac4C_metrics | Source code |
| add_default_metrics_v1 | Man page Source code |
| add_default_metrics_v2 | Man page Source code |
| add_diffNucToRefRatio | Source code |
| add_m1A_metrics | Source code |
| add_m3U_metrics | Source code |
| add_m5C_metrics | Source code |
| add_m7G_metrics | Source code |
| add_scoreA3p | Man page Source code |
| add_scoreA5p | Man page Source code |
| add_scoreA_3p | Source code |
| add_scoreA_5p | Source code |
| add_scoreC3p | Man page Source code |
| add_scoreC_3p | Source code |
| add_scoreZ_3p | Man page Source code |
| add_scoreZ_3p_util | Source code |
| alignSTAR | Man page Source code |
| all_comb_allNelements | Source code |
| bam2TxDT | Man page |
| bisGenome | Man page Source code |
| brainSTORM | Man page |
| brainSTORM-package | Man page |
| call_RNAmods_logRegMods | Man page Source code |
| check_whichRNAmods | Source code |
| deletion_rate | Source code |
| detect_2OmeScore | Source code |
| detect_ac4C | Source code |
| detect_m5C | Source code |
| extract_AUC_sen_spe | Source code |
| fastq_dupRate | Source code |
| fastq_nucFreq | Man page Source code |
| files_table | Source code |
| getGeneSeqsfromGenome | Source code |
| ggAlignEffPlot | Source code |
| gg_lce | Man page Source code |
| gg_nucFreq | Man page Source code |
| gg_readStats | Man page Source code |
| hasDups | Source code |
| hlp_assign_scores | Man page Source code |
| hlp_start_CALLS | Man page Source code |
| hlpr_add_REScols | Source code |
| hlpr_confusMatOutcome | Source code |
| is.2Ome | Source code |
| is.ac4C | Source code |
| is.m1A | Source code |
| is.m3U | Source code |
| is.m5C | Source code |
| is.m7G | Source code |
| is.pseudoU | Source code |
| libComplexReport | Man page Source code |
| m1A_scores | Man page |
| m3U_scores | Man page |
| m5C_scores | Man page |
| m7G_scores | Man page |
| mapSummPlot | Source code |
| matthewCorrCoeff | Source code |
| mkBedFromFastaTxOme | Man page |
| mkGTF | Source code |
| mkSTARgenome | Man page Source code |
| mkTmpDir | Source code |
| mkTranscriptome | Man page |
| rRNAmods_Sc_Taoka | Man page |
| reads_report | Man page Source code |
| rmTmpDir | Man page Source code |
| saveAsRDSIfNotAlready | Source code |
| scale_by_nuc | Source code |
| scoreA | Source code |
| scoreC_3p | Source code |
| scoreZ | Source code |
| storm_META | Man page Source code |
| storm_STORM | Man page |
| storm_add_scoreA3p | Man page Source code |
| storm_add_scoreA5p | Man page Source code |
| storm_add_scoreC3p | Man page |
| storm_assignScores | Man page Source code |
| storm_baseCols | Man page |
| storm_baseCoorCols | Man page |
| storm_calls | Source code |
| storm_confMatrix | Source code |
| storm_confMatrix4plot | Source code |
| storm_evalPreds | Man page Source code |
| storm_makeCalls | Source code |
| storm_metricsBoxPlot_byNuc | Man page Source code |
| storm_metricsScatterPlot_byPos | Man page Source code |
| storm_plot_confMat | Man page |
| storm_reduceToGA | Source code |
| storm_summary | Source code |
| trainLogModel_RNAmods | Source code |
| trainLogModel_allRNAmods | Source code |
| yeast_STORM | Man page |
