scsR (version 1.8.0)

SiRNA correction for seed mediated off-target effect

Description

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.

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Version

1.8.0

License

GPL-2

Maintainer

Andrea Franceschini Roger Meier rogermeierlmscethzch Christian von Mering meringimlsuzhch

Last Published

February 15th, 2017

Functions in scsR (1.8.0)

plot seeds utility methods

bydf

seed_correction_pooled

uuk_screen

cell number phenotype of the Uukuniemi QIAGEN siRNA genome wide screen

compare_sorted_geneSets

delete_undefined_rows

create_sd_matrix

miRBase_20

miRBase version 20 mature sequences (homo sapiens)

seed_correction

uuk_screen_dh

cell number phenotype of the Uukuniemi DHARMACON siRNA genome wide screen

seeds_analysis

intersectAll

benchmark_shared_hits

randomizeInner

removeSharedOffTargets

enrichment_heatmap

median_replicates

add_rank_col

replace_non_null_elements

transcribe_seqs

randomSortOnVal

renameColDf