chymera_paralog: Raw reads for paralog screen from CHyMErA paper

In HenryWard/orthrus: Scoring Combinatorial CRISPR Screens

Raw reads for paralog screen from CHyMErA paper

Description

A dataset containing raw read counts from a paralog-targeting library using the CHyMErA system, as described in Gonatopoulos-Pournatzis et al. (2020).

Usage

chymera_paralog

Format

A data frame with 92,746 rows and 32 variables:

ID

guide ID

Library

which library the guide belongs to, of "DualTargeting", "DualTargeting_NT", "Paralogs", or "DualTargeting_iCtrl"

gene1

gene targeted by Cas9

gene2

gene targeted by Cas12a

Cas9.Target.Site

genomic region targeted by Cas9

Cas9.Guide.Source

"TKOv3" if guide originated in TKOv3 library, otherwise "KRB" if made for this library

Cas9.Guide

Cas9 guide sequence

Cas9.Guide.Type

"exonic" if Cas9 targets an exonic region, "intergenic if it targets an intergenic region, "NT" if non-targeting

Cpf1.Target.Site

genomic region targeted by Cas12a

Cpf1.Guide

Cas9 guide sequence

Cpf1.Guide.Type

"exonic" if Cas9 targets an exonic region, "intergenic if it targets an intergenic region, "NT" if non-targeting

CNN.Score

score for guide quality based on CNN trained as described in paper mentioned above

HAP1.T0

raw read counts for HAP1 - Torin at T0

HAP1.T12A

raw read counts for HAP1 - Torin at T12, technical replicate A

HAP1.T12B

raw read counts for HAP1 - Torin at T12, technical replicate B

HAP1.T12C

raw read counts for HAP1 - Torin at T12, technical replicate C

HAP1.T18A

raw read counts for HAP1 - Torin at T18, technical replicate A

HAP1.T18B

raw read counts for HAP1 - Torin at T18, technical replicate B

HAP1.T18C

raw read counts for HAP1 - Torin at T18, technical replicate C

HAP1.Torin.T12A

raw read counts for HAP1 + Torin at T12, technical replicate A

HAP1.Torin.T12B

raw read counts for HAP1 + Torin at T12, technical replicate B

HAP1.Torin.T12C

raw read counts for HAP1 + Torin at T12, technical replicate C

HAP1.Torin.T18A

raw read counts for HAP1 + Torin at T18, technical replicate A

HAP1.Torin.T18B

raw read counts for HAP1 + Torin at T18, technical replicate B

HAP1.Torin.T18C

raw read counts for HAP1 + Torin at T18, technical replicate C

RPE1.T0

raw read counts for RPE1 at T0

RPE1.T18A

raw read counts for RPE1 at T18, technical replicate A

RPE1.T18B

raw read counts for RPE1 at T18, technical replicate B

RPE1.T18C

raw read counts for RPE1 at T18, technical replicate C

RPE1.T24A

raw read counts for RPE1 at T24, technical replicate A

RPE1.T24B

raw read counts for RPE1 at T24, technical replicate B

RPE1.T24C

raw read counts for RPE1 at T24, technical replicate C

Source

https://crispr.ccbr.utoronto.ca/chymera/

HenryWard/orthrus documentation built on June 2, 2023, 10:28 p.m.