diff --git a/DESCRIPTION b/DESCRIPTION index c188c51..63bb27f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: crisprDesign Title: Comprehensive design of CRISPR gRNAs for nucleases and base editors -Version: 0.99.177 +Version: 0.99.178 Authors@R: c( person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre")), person("Luke", "Hoberecht", email = "lukehob3@gmail.com", role = c("aut")) diff --git a/README.Rmd b/README.Rmd index b88b1f2..a76f777 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,7 +18,8 @@ Date: July 1, 2022 # Introduction `crisprDesign` is the core package of the -[crisprVerse](https://github.com/crisprVerse), and plays the role of a +[crisprVerse](https://github.com/crisprVerse) ecosystem, +and plays the role of a one-stop shop for designing and annotating CRISPR guide RNA (gRNA) sequences. This includes the characterization of on-targets and off-targets using different aligners, on- and off-target diff --git a/README.md b/README.md index c294d5b..1ee5328 100644 --- a/README.md +++ b/README.md @@ -63,9 +63,9 @@ Date: July 1, 2022 # Introduction `crisprDesign` is the core package of the -[crisprVerse](https://github.com/crisprVerse), and plays the role of a -one-stop shop for designing and annotating CRISPR guide RNA (gRNA) -sequences. This includes the characterization of on-targets and +[crisprVerse](https://github.com/crisprVerse) ecosystem, and plays the +role of a one-stop shop for designing and annotating CRISPR guide RNA +(gRNA) sequences. This includes the characterization of on-targets and off-targets using different aligners, on- and off-target scoring, gene context annotation, SNP annotation, sequence feature characterization, repeat annotation, and many more. @@ -416,7 +416,7 @@ guideSet <- addSequenceFeatures(guideSet) head(guideSet) ``` - ## GuideSet object with 6 ranges and 11 metadata columns: + ## GuideSet object with 6 ranges and 12 metadata columns: ## seqnames ranges strand | protospacer pam ## | ## spacer_107 chr12 67371 + | CCGAGTTGCTGCGCTGCTGC CGG @@ -433,14 +433,14 @@ head(guideSet) ## spacer_112 67396 67399 region_1 80 FALSE FALSE ## spacer_76 67244 67247 region_1 85 FALSE TRUE ## spacer_55 67153 67156 region_1 60 FALSE FALSE - ## polyG polyT startingGGGGG - ## - ## spacer_107 FALSE FALSE FALSE - ## spacer_9 FALSE FALSE FALSE - ## spacer_74 FALSE FALSE FALSE - ## spacer_112 FALSE FALSE FALSE - ## spacer_76 TRUE FALSE FALSE - ## spacer_55 FALSE FALSE FALSE + ## polyG polyT startingGGGGG NNGG + ## + ## spacer_107 FALSE FALSE FALSE CCGG + ## spacer_9 FALSE FALSE FALSE ATGG + ## spacer_74 FALSE FALSE FALSE ACGG + ## spacer_112 FALSE FALSE FALSE GGGG + ## spacer_76 TRUE FALSE FALSE CAGG + ## spacer_55 FALSE FALSE FALSE TGGG ## ------- ## seqinfo: 640 sequences (1 circular) from hg38 genome ## crisprNuclease: SpCas9 @@ -545,7 +545,7 @@ Let’s look at what was added to the `GuideSet`: guideSet ``` - ## GuideSet object with 20 ranges and 16 metadata columns: + ## GuideSet object with 20 ranges and 17 metadata columns: ## seqnames ranges strand | protospacer pam ## | ## spacer_107 chr12 67371 + | CCGAGTTGCTGCGCTGCTGC CGG @@ -572,32 +572,32 @@ guideSet ## spacer_24 67069 67072 region_1 80 FALSE FALSE ## spacer_13 66976 66979 region_1 60 FALSE FALSE ## spacer_95 67308 67305 region_1 60 FALSE TRUE - ## polyG polyT startingGGGGG n0 n1 n0_c - ## - ## spacer_107 FALSE FALSE FALSE 1 0 1 - ## spacer_9 FALSE FALSE FALSE 1 0 1 - ## spacer_74 FALSE FALSE FALSE 1 0 1 - ## spacer_112 FALSE FALSE FALSE 1 0 1 - ## spacer_76 TRUE FALSE FALSE 1 0 1 - ## ... ... ... ... ... ... ... - ## spacer_121 FALSE FALSE FALSE 1 0 1 - ## spacer_34 TRUE FALSE FALSE 1 0 1 - ## spacer_24 FALSE FALSE FALSE 1 0 1 - ## spacer_13 FALSE FALSE FALSE 1 0 1 - ## spacer_95 FALSE FALSE FALSE 1 0 1 - ## n1_c alignments - ## - ## spacer_107 0 chr12:67371:+ - ## spacer_9 0 chr12:66943:- - ## spacer_74 0 chr12:67233:+ - ## spacer_112 0 chr12:67396:- - ## spacer_76 0 chr12:67244:- - ## ... ... ... - ## spacer_121 0 chr12:67413:+ - ## spacer_34 0 chr12:67093:- - ## spacer_24 0 chr12:67069:- - ## spacer_13 0 chr12:66976:- - ## spacer_95 0 chr12:67308:+ + ## polyG polyT startingGGGGG NNGG n0 n1 + ## + ## spacer_107 FALSE FALSE FALSE CCGG 1 0 + ## spacer_9 FALSE FALSE FALSE ATGG 1 0 + ## spacer_74 FALSE FALSE FALSE ACGG 1 0 + ## spacer_112 FALSE FALSE FALSE GGGG 1 0 + ## spacer_76 TRUE FALSE FALSE CAGG 1 0 + ## ... ... ... ... ... ... ... + ## spacer_121 FALSE FALSE FALSE AGGG 1 0 + ## spacer_34 TRUE FALSE FALSE GGGG 1 0 + ## spacer_24 FALSE FALSE FALSE TGGG 1 0 + ## spacer_13 FALSE FALSE FALSE TGGG 1 0 + ## spacer_95 FALSE FALSE FALSE TGGG 1 0 + ## n0_c n1_c alignments + ## + ## spacer_107 1 0 chr12:67371:+ + ## spacer_9 1 0 chr12:66943:- + ## spacer_74 1 0 chr12:67233:+ + ## spacer_112 1 0 chr12:67396:- + ## spacer_76 1 0 chr12:67244:- + ## ... ... ... ... + ## spacer_121 1 0 chr12:67413:+ + ## spacer_34 1 0 chr12:67093:- + ## spacer_24 1 0 chr12:67069:- + ## spacer_13 1 0 chr12:66976:- + ## spacer_95 1 0 chr12:67308:+ ## ------- ## seqinfo: 640 sequences (1 circular) from hg38 genome ## crisprNuclease: SpCas9 @@ -718,7 +718,7 @@ guideSet <- addOffTargetScores(guideSet) guideSet ``` - ## GuideSet object with 17 ranges and 19 metadata columns: + ## GuideSet object with 17 ranges and 20 metadata columns: ## seqnames ranges strand | protospacer pam ## | ## spacer_107 chr12 67371 + | CCGAGTTGCTGCGCTGCTGC CGG @@ -745,32 +745,32 @@ guideSet ## spacer_24 67069 67072 region_1 80 FALSE FALSE ## spacer_13 66976 66979 region_1 60 FALSE FALSE ## spacer_95 67308 67305 region_1 60 FALSE TRUE - ## polyG polyT startingGGGGG n0 n1 n0_c - ## - ## spacer_107 FALSE FALSE FALSE 1 0 1 - ## spacer_9 FALSE FALSE FALSE 1 0 1 - ## spacer_74 FALSE FALSE FALSE 1 0 1 - ## spacer_112 FALSE FALSE FALSE 1 0 1 - ## spacer_76 TRUE FALSE FALSE 1 0 1 + ## polyG polyT startingGGGGG NNGG n0 n1 + ## + ## spacer_107 FALSE FALSE FALSE CCGG 1 0 + ## spacer_9 FALSE FALSE FALSE ATGG 1 0 + ## spacer_74 FALSE FALSE FALSE ACGG 1 0 + ## spacer_112 FALSE FALSE FALSE GGGG 1 0 + ## spacer_76 TRUE FALSE FALSE CAGG 1 0 + ## ... ... ... ... ... ... ... + ## spacer_71 FALSE FALSE FALSE GCGG 1 0 + ## spacer_121 FALSE FALSE FALSE AGGG 1 0 + ## spacer_24 FALSE FALSE FALSE TGGG 1 0 + ## spacer_13 FALSE FALSE FALSE TGGG 1 0 + ## spacer_95 FALSE FALSE FALSE TGGG 1 0 + ## n0_c n1_c alignments inRepeats score_cfd score_mit + ## + ## spacer_107 1 0 chr12:67371:+ FALSE 1 1 + ## spacer_9 1 0 chr12:66943:- FALSE 1 1 + ## spacer_74 1 0 chr12:67233:+ FALSE 1 1 + ## spacer_112 1 0 chr12:67396:- FALSE 1 1 + ## spacer_76 1 0 chr12:67244:- FALSE 1 1 ## ... ... ... ... ... ... ... - ## spacer_71 FALSE FALSE FALSE 1 0 1 - ## spacer_121 FALSE FALSE FALSE 1 0 1 - ## spacer_24 FALSE FALSE FALSE 1 0 1 - ## spacer_13 FALSE FALSE FALSE 1 0 1 - ## spacer_95 FALSE FALSE FALSE 1 0 1 - ## n1_c alignments inRepeats score_cfd score_mit - ## - ## spacer_107 0 chr12:67371:+ FALSE 1 1 - ## spacer_9 0 chr12:66943:- FALSE 1 1 - ## spacer_74 0 chr12:67233:+ FALSE 1 1 - ## spacer_112 0 chr12:67396:- FALSE 1 1 - ## spacer_76 0 chr12:67244:- FALSE 1 1 - ## ... ... ... ... ... ... - ## spacer_71 0 chr12:67218:- FALSE 1 1 - ## spacer_121 0 chr12:67413:+ FALSE 1 1 - ## spacer_24 0 chr12:67069:- FALSE 1 1 - ## spacer_13 0 chr12:66976:- FALSE 1 1 - ## spacer_95 0 chr12:67308:+ FALSE 1 1 + ## spacer_71 1 0 chr12:67218:- FALSE 1 1 + ## spacer_121 1 0 chr12:67413:+ FALSE 1 1 + ## spacer_24 1 0 chr12:67069:- FALSE 1 1 + ## spacer_13 1 0 chr12:66976:- FALSE 1 1 + ## spacer_95 1 0 chr12:67308:+ FALSE 1 1 ## ------- ## seqinfo: 640 sequences (1 circular) from hg38 genome ## crisprNuclease: SpCas9 @@ -843,7 +843,7 @@ guideSet <- addOnTargetScores(guideSet, methods="crisprater") head(guideSet) ``` - ## GuideSet object with 6 ranges and 20 metadata columns: + ## GuideSet object with 6 ranges and 21 metadata columns: ## seqnames ranges strand | protospacer pam ## | ## spacer_107 chr12 67371 + | CCGAGTTGCTGCGCTGCTGC CGG @@ -860,22 +860,22 @@ head(guideSet) ## spacer_112 67396 67399 region_1 80 FALSE FALSE ## spacer_76 67244 67247 region_1 85 FALSE TRUE ## spacer_55 67153 67156 region_1 60 FALSE FALSE - ## polyG polyT startingGGGGG n0 n1 n0_c - ## - ## spacer_107 FALSE FALSE FALSE 1 0 1 - ## spacer_9 FALSE FALSE FALSE 1 0 1 - ## spacer_74 FALSE FALSE FALSE 1 0 1 - ## spacer_112 FALSE FALSE FALSE 1 0 1 - ## spacer_76 TRUE FALSE FALSE 1 0 1 - ## spacer_55 FALSE FALSE FALSE 1 0 1 - ## n1_c alignments inRepeats score_cfd score_mit - ## - ## spacer_107 0 chr12:67371:+ FALSE 1 1 - ## spacer_9 0 chr12:66943:- FALSE 1 1 - ## spacer_74 0 chr12:67233:+ FALSE 1 1 - ## spacer_112 0 chr12:67396:- FALSE 1 1 - ## spacer_76 0 chr12:67244:- FALSE 1 1 - ## spacer_55 0 chr12:67153:- FALSE 1 1 + ## polyG polyT startingGGGGG NNGG n0 n1 + ## + ## spacer_107 FALSE FALSE FALSE CCGG 1 0 + ## spacer_9 FALSE FALSE FALSE ATGG 1 0 + ## spacer_74 FALSE FALSE FALSE ACGG 1 0 + ## spacer_112 FALSE FALSE FALSE GGGG 1 0 + ## spacer_76 TRUE FALSE FALSE CAGG 1 0 + ## spacer_55 FALSE FALSE FALSE TGGG 1 0 + ## n0_c n1_c alignments inRepeats score_cfd score_mit + ## + ## spacer_107 1 0 chr12:67371:+ FALSE 1 1 + ## spacer_9 1 0 chr12:66943:- FALSE 1 1 + ## spacer_74 1 0 chr12:67233:+ FALSE 1 1 + ## spacer_112 1 0 chr12:67396:- FALSE 1 1 + ## spacer_76 1 0 chr12:67244:- FALSE 1 1 + ## spacer_55 1 0 chr12:67153:- FALSE 1 1 ## score_crisprater ## ## spacer_107 0.782780 @@ -953,7 +953,7 @@ The gene annotation can be retrieved using the function geneAnnotation(guideSet) ``` - ## DataFrame with 17 rows and 23 columns + ## DataFrame with 17 rows and 24 columns ## chr anchor_site strand gene_symbol gene_id ## ## spacer_107 chr12 67368 + IQSEC3 ENSG00000120645 @@ -967,58 +967,71 @@ geneAnnotation(guideSet) ## spacer_24 chr12 67072 - IQSEC3 ENSG00000120645 ## spacer_13 chr12 66979 - IQSEC3 ENSG00000120645 ## spacer_95 chr12 67305 + IQSEC3 ENSG00000120645 - ## tx_id protein_id cut_cds cut_fiveUTRs cut_threeUTRs - ## - ## spacer_107 ENST00000538872 ENSP00000437554 TRUE FALSE FALSE - ## spacer_9 ENST00000538872 ENSP00000437554 TRUE FALSE FALSE - ## spacer_74 ENST00000538872 ENSP00000437554 TRUE FALSE FALSE - ## spacer_112 ENST00000538872 ENSP00000437554 TRUE FALSE FALSE - ## spacer_76 ENST00000538872 ENSP00000437554 TRUE FALSE FALSE - ## ... ... ... ... ... ... - ## spacer_71 ENST00000538872 ENSP00000437554 TRUE FALSE FALSE - ## spacer_121 ENST00000538872 ENSP00000437554 TRUE FALSE FALSE - ## spacer_24 ENST00000538872 ENSP00000437554 TRUE FALSE FALSE - ## spacer_13 ENST00000538872 ENSP00000437554 TRUE FALSE FALSE - ## spacer_95 ENST00000538872 ENSP00000437554 TRUE FALSE FALSE - ## cut_introns percentCDS aminoAcidIndex downtreamATG percentTx - ## - ## spacer_107 FALSE 13.7 162 1 8.5 - ## spacer_9 FALSE 1.8 22 0 2.5 - ## spacer_74 FALSE 9.8 116 0 6.5 - ## spacer_112 FALSE 14.6 173 1 8.9 - ## spacer_76 FALSE 10.3 122 0 6.8 - ## ... ... ... ... ... ... - ## spacer_71 FALSE 9.6 113 0 6.4 - ## spacer_121 FALSE 14.9 176 1 9.1 - ## spacer_24 FALSE 5.4 64 0 4.3 - ## spacer_13 FALSE 2.7 33 0 3.0 - ## spacer_95 FALSE 11.9 141 1 7.6 - ## nIsoforms totalIsoforms percentIsoforms isCommonExon nCodingIsoforms - ## - ## spacer_107 1 2 50 FALSE 1 - ## spacer_9 1 2 50 FALSE 1 - ## spacer_74 1 2 50 FALSE 1 - ## spacer_112 1 2 50 FALSE 1 - ## spacer_76 1 2 50 FALSE 1 - ## ... ... ... ... ... ... - ## spacer_71 1 2 50 FALSE 1 - ## spacer_121 1 2 50 FALSE 1 - ## spacer_24 1 2 50 FALSE 1 - ## spacer_13 1 2 50 FALSE 1 - ## spacer_95 1 2 50 FALSE 1 - ## totalCodingIsoforms percentCodingIsoforms isCommonCodingExon - ## - ## spacer_107 2 50 FALSE - ## spacer_9 2 50 FALSE - ## spacer_74 2 50 FALSE - ## spacer_112 2 50 FALSE - ## spacer_76 2 50 FALSE - ## ... ... ... ... - ## spacer_71 2 50 FALSE - ## spacer_121 2 50 FALSE - ## spacer_24 2 50 FALSE - ## spacer_13 2 50 FALSE - ## spacer_95 2 50 FALSE + ## tx_id protein_id exon_id cut_cds + ## + ## spacer_107 ENST00000538872 ENSP00000437554 ENSE00002310174 TRUE + ## spacer_9 ENST00000538872 ENSP00000437554 ENSE00002310174 TRUE + ## spacer_74 ENST00000538872 ENSP00000437554 ENSE00002310174 TRUE + ## spacer_112 ENST00000538872 ENSP00000437554 ENSE00002310174 TRUE + ## spacer_76 ENST00000538872 ENSP00000437554 ENSE00002310174 TRUE + ## ... ... ... ... ... + ## spacer_71 ENST00000538872 ENSP00000437554 ENSE00002310174 TRUE + ## spacer_121 ENST00000538872 ENSP00000437554 ENSE00002310174 TRUE + ## spacer_24 ENST00000538872 ENSP00000437554 ENSE00002310174 TRUE + ## spacer_13 ENST00000538872 ENSP00000437554 ENSE00002310174 TRUE + ## spacer_95 ENST00000538872 ENSP00000437554 ENSE00002310174 TRUE + ## cut_fiveUTRs cut_threeUTRs cut_introns percentCDS aminoAcidIndex + ## + ## spacer_107 FALSE FALSE FALSE 13.7 162 + ## spacer_9 FALSE FALSE FALSE 1.8 22 + ## spacer_74 FALSE FALSE FALSE 9.8 116 + ## spacer_112 FALSE FALSE FALSE 14.6 173 + ## spacer_76 FALSE FALSE FALSE 10.3 122 + ## ... ... ... ... ... ... + ## spacer_71 FALSE FALSE FALSE 9.6 113 + ## spacer_121 FALSE FALSE FALSE 14.9 176 + ## spacer_24 FALSE FALSE FALSE 5.4 64 + ## spacer_13 FALSE FALSE FALSE 2.7 33 + ## spacer_95 FALSE FALSE FALSE 11.9 141 + ## downtreamATG percentTx nIsoforms totalIsoforms percentIsoforms + ## + ## spacer_107 1 8.5 1 2 50 + ## spacer_9 0 2.5 1 2 50 + ## spacer_74 0 6.5 1 2 50 + ## spacer_112 1 8.9 1 2 50 + ## spacer_76 0 6.8 1 2 50 + ## ... ... ... ... ... ... + ## spacer_71 0 6.4 1 2 50 + ## spacer_121 1 9.1 1 2 50 + ## spacer_24 0 4.3 1 2 50 + ## spacer_13 0 3.0 1 2 50 + ## spacer_95 1 7.6 1 2 50 + ## isCommonExon nCodingIsoforms totalCodingIsoforms + ## + ## spacer_107 FALSE 1 2 + ## spacer_9 FALSE 1 2 + ## spacer_74 FALSE 1 2 + ## spacer_112 FALSE 1 2 + ## spacer_76 FALSE 1 2 + ## ... ... ... ... + ## spacer_71 FALSE 1 2 + ## spacer_121 FALSE 1 2 + ## spacer_24 FALSE 1 2 + ## spacer_13 FALSE 1 2 + ## spacer_95 FALSE 1 2 + ## percentCodingIsoforms isCommonCodingExon + ## + ## spacer_107 50 FALSE + ## spacer_9 50 FALSE + ## spacer_74 50 FALSE + ## spacer_112 50 FALSE + ## spacer_76 50 FALSE + ## ... ... ... + ## spacer_71 50 FALSE + ## spacer_121 50 FALSE + ## spacer_24 50 FALSE + ## spacer_13 50 FALSE + ## spacer_95 50 FALSE It contains a lot of information that contextualizes the genomic location of the protospacer sequences. @@ -1142,7 +1155,7 @@ guideSet <- guideSet[o] head(guideSet) ``` - ## GuideSet object with 6 ranges and 25 metadata columns: + ## GuideSet object with 6 ranges and 26 metadata columns: ## seqnames ranges strand | protospacer pam ## | ## spacer_9 chr12 66943 - | GCTCTGCTGGTTCTGCACGA TGG @@ -1159,22 +1172,22 @@ head(guideSet) ## spacer_74 67233 67230 region_1 80 FALSE FALSE ## spacer_76 67244 67247 region_1 85 FALSE TRUE ## spacer_121 67413 67410 region_1 75 FALSE TRUE - ## polyG polyT startingGGGGG n0 n1 n0_c - ## - ## spacer_9 FALSE FALSE FALSE 1 0 1 - ## spacer_112 FALSE FALSE FALSE 1 0 1 - ## spacer_107 FALSE FALSE FALSE 1 0 1 - ## spacer_74 FALSE FALSE FALSE 1 0 1 - ## spacer_76 TRUE FALSE FALSE 1 0 1 - ## spacer_121 FALSE FALSE FALSE 1 0 1 - ## n1_c alignments inRepeats score_cfd score_mit - ## - ## spacer_9 0 chr12:66943:- FALSE 1 1 - ## spacer_112 0 chr12:67396:- FALSE 1 1 - ## spacer_107 0 chr12:67371:+ FALSE 1 1 - ## spacer_74 0 chr12:67233:+ FALSE 1 1 - ## spacer_76 0 chr12:67244:- FALSE 1 1 - ## spacer_121 0 chr12:67413:+ FALSE 1 1 + ## polyG polyT startingGGGGG NNGG n0 n1 + ## + ## spacer_9 FALSE FALSE FALSE ATGG 1 0 + ## spacer_112 FALSE FALSE FALSE GGGG 1 0 + ## spacer_107 FALSE FALSE FALSE CCGG 1 0 + ## spacer_74 FALSE FALSE FALSE ACGG 1 0 + ## spacer_76 TRUE FALSE FALSE CAGG 1 0 + ## spacer_121 FALSE FALSE FALSE AGGG 1 0 + ## n0_c n1_c alignments inRepeats score_cfd score_mit + ## + ## spacer_9 1 0 chr12:66943:- FALSE 1 1 + ## spacer_112 1 0 chr12:67396:- FALSE 1 1 + ## spacer_107 1 0 chr12:67371:+ FALSE 1 1 + ## spacer_74 1 0 chr12:67233:+ FALSE 1 1 + ## spacer_76 1 0 chr12:67244:- FALSE 1 1 + ## spacer_121 1 0 chr12:67413:+ FALSE 1 1 ## score_crisprater enzymeAnnotation geneAnnotation ## ## spacer_9 0.834319 FALSE:FALSE:FALSE:... chr12:66946:-:... @@ -1206,7 +1219,7 @@ guideSet <- guideSet[o] head(guideSet) ``` - ## GuideSet object with 6 ranges and 25 metadata columns: + ## GuideSet object with 6 ranges and 26 metadata columns: ## seqnames ranges strand | protospacer pam ## | ## spacer_9 chr12 66943 - | GCTCTGCTGGTTCTGCACGA TGG @@ -1223,22 +1236,22 @@ head(guideSet) ## spacer_74 67233 67230 region_1 80 FALSE FALSE ## spacer_76 67244 67247 region_1 85 FALSE TRUE ## spacer_121 67413 67410 region_1 75 FALSE TRUE - ## polyG polyT startingGGGGG n0 n1 n0_c - ## - ## spacer_9 FALSE FALSE FALSE 1 0 1 - ## spacer_112 FALSE FALSE FALSE 1 0 1 - ## spacer_107 FALSE FALSE FALSE 1 0 1 - ## spacer_74 FALSE FALSE FALSE 1 0 1 - ## spacer_76 TRUE FALSE FALSE 1 0 1 - ## spacer_121 FALSE FALSE FALSE 1 0 1 - ## n1_c alignments inRepeats score_cfd score_mit - ## - ## spacer_9 0 chr12:66943:- FALSE 1 1 - ## spacer_112 0 chr12:67396:- FALSE 1 1 - ## spacer_107 0 chr12:67371:+ FALSE 1 1 - ## spacer_74 0 chr12:67233:+ FALSE 1 1 - ## spacer_76 0 chr12:67244:- FALSE 1 1 - ## spacer_121 0 chr12:67413:+ FALSE 1 1 + ## polyG polyT startingGGGGG NNGG n0 n1 + ## + ## spacer_9 FALSE FALSE FALSE ATGG 1 0 + ## spacer_112 FALSE FALSE FALSE GGGG 1 0 + ## spacer_107 FALSE FALSE FALSE CCGG 1 0 + ## spacer_74 FALSE FALSE FALSE ACGG 1 0 + ## spacer_76 TRUE FALSE FALSE CAGG 1 0 + ## spacer_121 FALSE FALSE FALSE AGGG 1 0 + ## n0_c n1_c alignments inRepeats score_cfd score_mit + ## + ## spacer_9 1 0 chr12:66943:- FALSE 1 1 + ## spacer_112 1 0 chr12:67396:- FALSE 1 1 + ## spacer_107 1 0 chr12:67371:+ FALSE 1 1 + ## spacer_74 1 0 chr12:67233:+ FALSE 1 1 + ## spacer_76 1 0 chr12:67244:- FALSE 1 1 + ## spacer_121 1 0 chr12:67413:+ FALSE 1 1 ## score_crisprater enzymeAnnotation geneAnnotation ## ## spacer_9 0.834319 FALSE:FALSE:FALSE:... chr12:66946:-:... @@ -2098,8 +2111,8 @@ sessionInfo() ## [5] Biostrings_2.65.3 XVector_0.37.1 ## [7] GenomicRanges_1.49.1 GenomeInfoDb_1.33.7 ## [9] IRanges_2.31.2 S4Vectors_0.35.3 - ## [11] BiocGenerics_0.43.4 crisprDesign_0.99.140 - ## [13] crisprBase_1.1.5 + ## [11] BiocGenerics_0.43.4 crisprDesign_0.99.176 + ## [13] crisprBase_1.1.8 ## ## loaded via a namespace (and not attached): ## [1] bitops_1.0-7 matrixStats_0.62.0 diff --git a/vignettes/intro.Rmd b/vignettes/intro.Rmd index 03f0ad2..c22cf3e 100644 --- a/vignettes/intro.Rmd +++ b/vignettes/intro.Rmd @@ -25,7 +25,8 @@ bibliography: references.bib # Introduction `crisprDesign` is the core package of the -[crisprVerse](https://github.com/crisprVerse), and plays the role of a +[crisprVerse](https://github.com/crisprVerse) ecosystem, +and plays the role of a one-stop shop for designing and annotating CRISPR guide RNA (gRNA) sequences. This includes the characterization of on-targets and off-targets using different aligners, on- and off-target