scsR: SiRNA correction for seed mediated off-target effect

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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.

Author
Andrea Franceschini
Date of publication
None
Maintainer
Andrea Franceschini <andrea.franceschini@isb-sib.ch>, Roger Meier <roger.meier@lmsc.ethz.ch>, Christian von Mering <mering@imls.uzh.ch>
License
GPL-2
Version
1.10.0

View on Bioconductor

Man pages

add_rank_col
add_rank_col
add_seed
add_seed
benchmark_shared_hits
benchmark_shared_hits
bydf
bydf
check_consistency
check_consistency
compare_sorted_geneSets
compare_sorted_geneSets
create_sd_matrix
create_sd_matrix
delColDf
delColDf
delete_undefined_rows
delete_undefined_rows
enrichment_geneSet
enrichment_geneSet
enrichment_heatmap
enrichment_heatmap
get_sd_quant
get_sd_quant
get_seed_oligos_df
get_seed_oligos_df
intersectAll
intersectAll
launch_RSA
launch_RSA
median_replicates
median_replicates
miRBase_20
miRBase version 20 mature sequences (homo sapiens)
OPIrsa
OPIrsa
OPIrsaScore
OPIrsaScore
plot_screen_hits
plot_screen_hits
plot_seeds_methods
plot seeds utility methods
randomizeInner
randomizeInner
randomSortOnVal
randomSortOnVal
removeSharedOffTargets
removeSharedOffTargets
renameColDf
renameColDf
replace_non_null_elements
replace_non_null_elements
seed_correction
seed_correction
seed_correction_pooled
seed_correction_pooled
seed_removal
seed_removal
seeds_analysis
seeds_analysis
sortInner
sortInner
split_df
split_df
transcribe_seqs
transcribe_seqs
uuk_screen
cell number phenotype of the Uukuniemi QIAGEN siRNA genome...
uuk_screen_dh
cell number phenotype of the Uukuniemi DHARMACON siRNA genome...

Files in this package

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