Man pages for shkonishi/rskoseq
This is my personal package of R functions for NGS data
| deg | Differential Expression Gene extraction using TCC package |
| fetch_bmt | Fetch data sets from biomart data base |
| fqfilter | Filtering and trimming of fastq files using ShortRead package |
| gc_read | GC content per read |
| genome_summary | Summary of genomic sequences from fasta file |
| ggblast | Simple visualization of local blast search output |
| gg_qa | Quality assesment with ShortRead package and return ggplot... |
| kmer_strm | Counting kmer of nucleotide sequence |
| maprate | Parse hisat2 or bowtie2 log file |
| nx | Calcuration of NX and LX from genome sequence. |
| project_rnsq | Create directory for RNA-seq pipeline |
| rawfqext | rawfqext |
| rblast | Local blast search with outfmt 6 |
| rep_hisat2 | Replicate execution of read alignment using hisat2 |
| rep_rsem | Continuous execution of sequence alignment using RSEM |
| rep_stringtie | Consecutive execution of Transcript assembly and... |
| revcomp | Reverse and/or Complement of Nucleotide sequence as character... |
| tcc_norm | Normarization of RNA-seq count data using tmm |
| vcf_utls | The utility for handling VCF |
