scsR: SiRNA correction for seed mediated off-target effect

Corrects genome-wide siRNA screens for seed mediated off-target effect. Suitable functions to identify the effective seeds/miRNAs and to visualize their effect are also provided in the package.

AuthorAndrea Franceschini
Date of publicationNone
MaintainerAndrea Franceschini <andrea.franceschini@isb-sib.ch>, Roger Meier <roger.meier@lmsc.ethz.ch>, Christian von Mering <mering@imls.uzh.ch>
LicenseGPL-2
Version1.10.0

View on Bioconductor

Functions

add_rank_col Man page
add_seed Man page
benchmark_shared_hits Man page
bydf Man page
bydfa Man page
check_consistency Man page
compare_sorted_geneSets Man page
create_sd_matrix Man page
delColDf Man page
delete_undefined_rows Man page
enrichment_geneSet Man page
enrichment_heatmap Man page
get_sd_quant Man page
get_seed_oligos_df Man page
intersectAll Man page
launch_RSA Man page
median_replicates Man page
miRBase_20 Man page
OPIrsa Man page
OPIrsaScore Man page
plot_effective_seeds_head Man page
plot_screen_hits Man page
plot_screen_seeds_count Man page
plot_seed_score_sd Man page
plot_seeds_oligo_count Man page
randomizeInner Man page
randomSortOnVal Man page
removeSharedOffTargets Man page
renameColDf Man page
replace_non_null_elements Man page
seed_correction Man page
seed_correction_pooled Man page
seed_removal Man page
seeds_analysis Man page
sortInner Man page
split_df Man page
transcribe_seqs Man page
uuk_screen Man page
uuk_screen_dh Man page

Files

scsR/DESCRIPTION
scsR/NAMESPACE
scsR/R
scsR/R/scsR.R scsR/R/scsR_plots.R scsR/R/scsR_utils.R
scsR/build
scsR/build/vignette.rds
scsR/data
scsR/data/datalist
scsR/data/miRBase_20.rda
scsR/data/uuk_screen.rda
scsR/data/uuk_screen_dh.rda
scsR/inst
scsR/inst/doc
scsR/inst/doc/scsR.R
scsR/inst/doc/scsR.Rnw
scsR/inst/doc/scsR.pdf
scsR/man
scsR/man/OPIrsa.Rd scsR/man/OPIrsaScore.Rd scsR/man/add_rank_col.Rd scsR/man/add_seed.Rd scsR/man/benchmark_shared_hits.Rd scsR/man/bydf.Rd scsR/man/check_consistency.Rd scsR/man/compare_sorted_geneSets.Rd scsR/man/create_sd_matrix.Rd scsR/man/delColDf.Rd scsR/man/delete_undefined_rows.Rd scsR/man/enrichment_geneSet.Rd scsR/man/enrichment_heatmap.Rd scsR/man/get_sd_quant.Rd scsR/man/get_seed_oligos_df.Rd scsR/man/intersectAll.Rd scsR/man/launch_RSA.Rd scsR/man/median_replicates.Rd scsR/man/miRBase_20.Rd scsR/man/plot_screen_hits.Rd scsR/man/plot_seeds_methods.Rd scsR/man/randomSortOnVal.Rd scsR/man/randomizeInner.Rd scsR/man/removeSharedOffTargets.Rd scsR/man/renameColDf.Rd scsR/man/replace_non_null_elements.Rd scsR/man/seed_correction.Rd scsR/man/seed_correction_pooled.Rd scsR/man/seed_removal.Rd scsR/man/seeds_analysis.Rd scsR/man/sortInner.Rd scsR/man/split_df.Rd scsR/man/transcribe_seqs.Rd scsR/man/uuk_screen.Rd scsR/man/uuk_screen_dh.Rd
scsR/vignettes
scsR/vignettes/effective_seeds_head1.pdf
scsR/vignettes/screen_hits.pdf
scsR/vignettes/screen_hits_corrected.pdf
scsR/vignettes/screen_hits_seed_removal.pdf
scsR/vignettes/screen_seeds_count1.pdf
scsR/vignettes/scsR.Rnw
scsR/vignettes/seed_score_sd.pdf
scsR/vignettes/seeds_oligo_count1.pdf
scsR/vignettes/uuk_benchmark_sh.pdf
scsR/vignettes/uuk_benchmark_sh_pooled.pdf
scsR/vignettes/uuk_enrichment_heatmap.pdf
scsR/vignettes/uuk_enrichment_heatmap_pooled.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.