Man pages for bioDS/phyloRNA
Tools for phylogenetic analyses of scRNAseq data
| abspath | Turn path into an absolute path |
| all_files_exist | Check if all specified files exist |
| bamtagregex | Change sam/bam tag values |
| bamtofastq | BAM to fastq |
| cellranger_count | Estimate scRNAseq Gene Expression with Cellranger Count |
| cellranger_mkref | Generate Cellranger Transcriptome Reference Genome |
| convert | Convert object or its items into a requested type |
| corename | Get core part of the file name |
| densest_subset | Find the densest subset of a matrix |
| expr | Functions for manipulation with the expression data |
| filter_gtf | Filter GTF file according to index file |
| GATK | Mapping to the Genome Analysis ToolKit (GATK) |
| gatk_mutect2 | Mapping to the Mutect2 |
| gatk_pon | Make a Panel of Normals using the GATK toolkit |
| gatk_prepare | Prepare sam/bam file according to GATK |
| GATKR6 | GATK binding as an R6 class |
| gatk_snv | Identify and filter SNVs |
| hdi | Calculate the highest density interval |
| IndexedVector | Indexed vector |
| is_nn | Check if value is NULL or NA |
| missing_to_na | Convert a value to NA |
| mkdir | Create directory |
| phyloRNA | phyloRNA: A package for phylogenetical analysis of RNA data |
| random_string | Create a random string |
| read_column | Read a column from a delimited file |
| read_fasta | Read fasta file |
| remap | Remap BAM file to a new reference genome |
| remove_constant | Remove constant |
| replace | Replace values in a vector or a matrix |
| replace_ordinal | Replace missing categories on ordinal scale |
| seq2tab | Convert sequences into a table |
| systemE | Run an external command |
| tab2seq | Convert a table into a vector of sequences |
| vcftools_filter | Filter VCF file |
| vcm | Make a variant call matrix |
| write_fasta | Write fasta file |
