scphaser: Phase Variants Within Genes Using Allele Counts

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Phase variants within genes using allele counts from single-cell RNA-seq data.

Author
Daniel Edsgärd [aut, cre]
Date of publication
2016-08-31 14:54:45
Maintainer
Daniel Edsgärd <edsgard@hotmail.com>
License
GPL-3
Version
1.0.0
URLs

View on CRAN

Man pages

call_gt
Call transcribed genotypes
filter_acset
Filter variants and features
filter_feat_nminvar
Filter features on minimal number of required variants
filter_homovars
Filter homozygous variants
filter_var_gt
Filter variants
filter_zerorow
Filter variants with zero allele counts in all cells
marinov
Single-cell RNA-seq allele counts for the Marinov et al...
mousehybrid
Single-cell RNA-seq allele counts for a mouse-hybrid dataset
new_acset
Construct an allele count set
phase
Phasing of alleles
plot_conc
Phasing concordance plot
racset
Randomize an acset
set_gt_conc
Cell-distribution variability upon phasing
subset_cols
Subset cells
subset_feat
Subset features
subset_rows
Subset variants

Files in this package

scphaser
scphaser/inst
scphaser/inst/CITATION
scphaser/inst/doc
scphaser/inst/doc/scphaser.html
scphaser/inst/doc/scphaser.R
scphaser/inst/doc/refman.pdf
scphaser/inst/doc/scphaser.Rmd
scphaser/inst/doc/LICENSE
scphaser/tests
scphaser/tests/testthat.R
scphaser/tests/testthat
scphaser/tests/testthat/test-phasing.R
scphaser/tests/testthat/test-performance.R
scphaser/NAMESPACE
scphaser/data
scphaser/data/mousehybrid.rda
scphaser/data/marinov.rda
scphaser/R
scphaser/R/scphaser.R
scphaser/R/data.R
scphaser/R/performance.R
scphaser/vignettes
scphaser/vignettes/scphaser.Rmd
scphaser/README.md
scphaser/MD5
scphaser/build
scphaser/build/vignette.rds
scphaser/DESCRIPTION
scphaser/man
scphaser/man/racset.Rd
scphaser/man/set_gt_conc.Rd
scphaser/man/mousehybrid.Rd
scphaser/man/filter_homovars.Rd
scphaser/man/subset_feat.Rd
scphaser/man/plot_conc.Rd
scphaser/man/subset_cols.Rd
scphaser/man/new_acset.Rd
scphaser/man/marinov.Rd
scphaser/man/call_gt.Rd
scphaser/man/filter_zerorow.Rd
scphaser/man/filter_feat_nminvar.Rd
scphaser/man/filter_var_gt.Rd
scphaser/man/filter_acset.Rd
scphaser/man/subset_rows.Rd
scphaser/man/phase.Rd