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phyloRNA

phyloRNA is an utility package that maps functionality of a commonly used software to easy building phylogenetic trees from scRNAseq data.

Installation

devtools::install_github("biods/phyloRNA")

External software

For full functionality, following external software is also required:

  • cellranger: analyse 10X scRNA-seq data
  • bamtofastq: convert previously mapped BAM into fastq files
  • gatk: various BAM processing and variant detection
  • vcftools: filter out Variant Coding Files (VCF)
  • python3: utilize the pysam library for following scripts:
    • vcm.py: call scRNA-seq variants
    • bamtagregex.py: regex for sam/bam tags
  • gzip: compress output stream from vcftools

Install cellranger and bamtofastq from respective websites. To install gatk, vcftools and python3, you might consider the conda package manager. On UNIX-based OS, gzip should be already part of your distribution. Note that cellranger does not support Mac or Windows OS.

Once python3 is installed, you can install pysam by runing:

pip3 install pysam

Examples:

Here are but few examples of phyloRNA functionality:

Prepare foo.bam according to GATK best practices:

library("phyloRNA")
bam = GATKR6$new("foo.bam", "bar.fas","baz.vcf")
bam$(SortSam()$SplitNCigarReads()$Recalibrate()

Preprocess 10X expression data:

library("phyloRNA")
expr = expr_read10xh5("foo.h5")
expr = expr_quality_filter(expr, minUMI=500, minGene=250)
expr = expr_normalize(expr)
expr = expr_scale(data)

Remove columns and rows of data matrix with small amount of data

library("phyloRNA")
result = densest_subset(foo, density=0.5)

# delted rows
result$deleted_rows

# deleted columns
result$deleted_columns

# filtered matrix:
result$result