Man pages for Danis102/seqpac
Seqpac: A Framework for smallRNA analysis in R using Sequence-Based Counts
| add_reanno | Generates biotype annotation from reannotation object |
| anno | anno(PAC) Access the annotation table in S4 PAC |
| as.PAC | Converts an S3 PAC into a S4 PAC |
| as.reanno | Converts an S3 reanno into a S4 reanno |
| colnames | sample names |
| counts | counts(PAC) |
| create_PAC | Wrapper for creation of PAC object |
| filtsep_bin | Binary converter for PAC_filtsep |
| full | full(reanno) |
| import_reanno | Imports annotation from reannotation mapping |
| length | number of objects in PAC |
| make_conv | Create reference genome conversion table |
| make_counts | Make a count table |
| make_cutadapt | Trims/filter fastq using external... |
| make_PAC | Make PAC |
| make_pheno | Make Phenotype File |
| make_reanno | Makes annotation from R imported reannotation mapping |
| make_trim | Make trimmed and quality filtered fastq files |
| map_rangetype | Interval classification. |
| map_reanno | Aligning sequences against references using bowtie |
| merge_lanes | Merge fastq lane files |
| names | names of objects in reanno |
| ncol | number of samples |
| norm | norm(PAC) |
| nrow | number of sequences |
| overview | overview(reanno) |
| PAC | S4 object for PAC |
| PAC_check | Checks PAC format |
| PAC_covplot | Plot sequence coverage over a reference |
| PAC_deseq | A wrapper to DESeq2 that apply differential expression... |
| PAC_filter | Filter a PAC object on sequence size and coverage |
| PAC_filtsep | Generates filtered sequence name list seperated on group |
| PAC_gtf | Annotate against a GTF file |
| PAC_jitter | Plots jitter plot from PAC object |
| PAC_mapper | Advanced sequence mapping of a PAC object |
| PAC_nbias | Generates a nucleotide bias analysis from a PAC object |
| PAC_norm | Generates normalized values from a PAC object |
| PAC_pca | Principle component analysis with scatterplots from PAC |
| PAC_pie | Pie plot from PAC |
| PAC_saturation | Filter a PAC object on sequence size and coverage |
| PAC_sizedist | Generates size distribution plots from a PAC object |
| PAC_stackbar | Plot stackbars from PAC |
| PAC_summary | Summarizes PAC objects |
| PAC_trna | tsRNA analysis of PAC object |
| pheno | pheno(PAC) |
| reanno | S4 object for reanno output |
| rownames | sequence names |
| show | show(PAC) |
| simplify_reanno | Generates one-hit hierarchial biotype annotation |
| summary | summary(PAC) |
| tRNA_class | Classify tsRNA/tRFs from PAC object |
