Man pages for AngelCampos/tx_tools
An R package facilitating analysis of RNA modifications, structures, and interactions
| annotSites_RRACH | RRACH sites annotation D. melanogaster |
| bam_sk1 | Genomic Alignments example - Sk1 yeast |
| gA_sk1 | Gene annotation example - Sk1 yeast |
| genome_sk1 | Genome example - Sk1 yeast |
| getDumpedAlignments | Retrieve dumped alignments |
| hid_aggregate_DTlist | Merge lists of data.tables |
| hlp_coverageTab_mc | Calculate coverage table (coverage, ends, starts) for all... |
| hlp_genCoorTab_mc | Coordinate system table generator |
| hlp_nucFreqTab_mc | Calculate nucleotide frequency pileup for all gene models |
| hlp_plot_metageneRegions | Plot an extracted metaGeneMatrix |
| IUPAC_code_2nucs | IUPAC ambiguity alphabet (2nc) |
| IUPAC_CODE_MAP_extended | IUPAC code extended to consider deletions |
| IUPAC_code_simpl | Simplified nucleotide alphabet |
| mm_geneAnnot | Download gene annotation - Case study # 2 |
| sc_faGenome | Download genome to temporary file - Case study # 1 |
| sc_geneAnnot | Download gene annotation - Case study #1 |
| sc_rRNAmods_Taoka | Sk1 rRNA modifications catalogue |
| sc_txDTL | txtools-processed data - Case study # 1 |
| tk_faGenome | Download genome to temporary file - Case study # 3 |
| tk_geneAnnot | Download gene annotation - Case study # 3 |
| tx_add_diffNucToRef | Add number of nucleotide reads different to the reference... |
| tx_add_diffNucToRefRatio | Add different nucleotide reads to total ratio |
| tx_add_endRatio | Add ends to coverage ratio 1 bp downstream |
| tx_add_endRatio1bpDS | Add ends to coverage ratio 1bp down-stream |
| tx_add_endRatio1bpUS | Add ends to coverage ratio 1bp up-stream |
| tx_add_exonNumber | Add exon number |
| tx_add_exonPlace | Add exon place |
| tx_add_geneRegion | Add gene regions |
| tx_add_misincCount | Add counts of nucleotide reads different to the reference... |
| tx_add_misincRate | Add misincorporation to total nucleotide reads ratio |
| tx_add_misincRateNucSpec | Nucleotide specific misincorporation rate |
| tx_add_motifPresence | Add motif presence |
| tx_add_nucTotal | Add total number of nucleotide reads |
| tx_add_pos | Add position unique names |
| tx_add_refSeqDT | Add reference sequence to a data.table |
| tx_add_relTxPos | Add relative position in transcript |
| tx_add_rollingMean | Add rolling mean |
| tx_add_siteAnnotation | Add 1bp-site logical annotation |
| tx_add_spliceSitesLogical | Add SpliceSites |
| tx_add_startRatio | Add starts to coverage ratio |
| tx_add_startRatio1bpDS | Add starts to coverage ratio 1 bp downstream |
| tx_add_startRatio1bpUS | Add starts to coverage ratio 1 bp upstream |
| tx_combineTxReads | Combine txreads |
| tx_complete_DT | Complete a DT object missing genes |
| txCoreCols | txtools' core cols |
| txCoreCols_refSeq | txtools' core cols and refSeq |
| tx_counts | Total counts of reads per gene model |
| tx_cutEnds_DT | Cutting 5' and 3' ends of data.table using txcoors |
| tx_cut_geneAnnotBytxDT | Cut gene annotation by txDT's genes |
| tx_data_caseStudy2 | Load data - Case study #2 |
| tx_dm3_geneAnnot | D. melanogaster gene annotation subset path |
| txDTL_Tk | txtools-processed data - Case study # 3 |
| tx_extend_UTR | Extending GRanges 5' and 3' UTR blocks |
| tx_filter_maxWidth | Filter ranges by a maximum width |
| tx_generatePairedEndFASTQ | Generate paired-end FASTQ file |
| tx_generateSingleEndFASTQ | Generate single-end FASTQ file |
| tx_get_flankSequence | Get flanking sequences |
| tx_get_flanksFromLogicAnnot | Get data from a position and their neighboring positions |
| tx_get_geneLengths | Get length of genes |
| tx_get_metageneAtCDS | Get metagene at CDS |
| tx_get_metageneExons | Get metagene by exons |
| tx_get_metageneRegions | Get metagene regions |
| tx_get_transcriptSeqs | Get transcriptome sequences |
| tx_get_unassignedAlignments | Retrieve dumped alignments |
| tx_load_bam | Read paired end bam file by yield size |
| tx_load_bed | Load gene models from bed-12 and bed-6 files |
| tx_load_genome | Load genome |
| tx_load_rdsDT | Loading RDS files into data.tables |
| tx_makeDT_coverage | Summarized Coverage data.table |
| tx_makeDT_covNucFreq | Summarized Coverage & Nucleotide Frequency data.table |
| tx_makeDT_nucFreq | Summarized Nucleotide Frequency data.table |
| tx_merge_DT | Merge data.tables in list to a single data.table |
| tx_orderDT | Order txDT |
| tx_plot_ggseqlogo | Plot motif centered in logical annotation |
| tx_plot_metageneAtCDS | Plot metagene at CDS |
| tx_plot_metaGeneByBins | Plot metagene by bins |
| tx_plot_metageneExons | Plot metagene exons |
| tx_plot_metageneRegions | Plot metagene by regions |
| tx_plot_nucFreq | Nucleotide frequency plot |
| tx_plot_numeric | Numeric plot |
| tx_plot_staEndCov | Transcript coverage plot highlighting read-starts and... |
| tx_reads | Transcriptomic reads convertion |
| tx_sampleByGenes | Sample txDT by genes |
| tx_sample_GRList | Sampling alignments |
| tx_shift_geneWise | Shift column in txDT |
| tx_split_DT | Split data.table to list of data.tables |
| tx_test_LRTedgeR | Likelihood Ratio Test |
| tx_test_ttest | t-test in txDT list |
| txtools | txtools: A package facilitating analysis of RNA... |
| tx_unifyTxDTL | Unify lists of txDTs |
| window_around | Centered numeric sequence |
