| ... | ... |
@@ -1,6 +1,8 @@ |
| 1 | 1 |
--- |
| 2 | 2 |
title: "crisprScore: on-target and off-target scoring for CRISPR gRNAs" |
| 3 |
-output: github_document |
|
| 3 |
+output: |
|
| 4 |
+ github_document: |
|
| 5 |
+ toc: true |
|
| 4 | 6 |
bibliography: vignettes/references.bib |
| 5 | 7 |
--- |
| 6 | 8 |
|
| ... | ... |
@@ -512,9 +514,20 @@ input <- paste0(flank5, spacer, pam, flank3) |
| 512 | 514 |
results <- getLindelScores(input) |
| 513 | 515 |
``` |
| 514 | 516 |
|
| 517 |
+# License |
|
| 518 |
+ |
|
| 519 |
+The project as a whole is covered by the MIT license. The code for all |
|
| 520 |
+underlying Python packages, with their original licenses, can be found in |
|
| 521 |
+`inst/python`. We made sure that all licenses are compatible with the MIT |
|
| 522 |
+license and to indicate changes that we have made to the original code. |
|
| 523 |
+ |
|
| 524 |
+# Reproducibility |
|
| 525 |
+ |
|
| 515 | 526 |
```{r}
|
| 516 | 527 |
sessionInfo() |
| 517 | 528 |
``` |
| 518 | 529 |
|
| 530 |
+ |
|
| 531 |
+ |
|
| 519 | 532 |
# References |
| 520 | 533 |
|
| ... | ... |
@@ -1,6 +1,38 @@ |
| 1 | 1 |
crisprScore: on-target and off-target scoring for CRISPR gRNAs |
| 2 | 2 |
================ |
| 3 | 3 |
|
| 4 |
+- [Overview](#overview) |
|
| 5 |
+- [Installation and getting |
|
| 6 |
+ started](#installation-and-getting-started) |
|
| 7 |
+ - [Software requirements](#software-requirements) |
|
| 8 |
+ - [OS Requirements](#os-requirements) |
|
| 9 |
+ - [R Dependencies](#r-dependencies) |
|
| 10 |
+ - [Installation](#installation) |
|
| 11 |
+- [Getting started](#getting-started) |
|
| 12 |
+- [On-targeting efficiency scores](#on-targeting-efficiency-scores) |
|
| 13 |
+ - [Cas9 methods](#cas9-methods) |
|
| 14 |
+ - [Rule Set 1](#rule-set-1) |
|
| 15 |
+ - [Azimuth](#azimuth) |
|
| 16 |
+ - [Rule Set 3](#rule-set-3) |
|
| 17 |
+ - [DeepHF](#deephf) |
|
| 18 |
+ - [DeepSpCas9](#deepspcas9) |
|
| 19 |
+ - [CRISPRscan](#crisprscan) |
|
| 20 |
+ - [CRISPRater](#crisprater) |
|
| 21 |
+ - [CRISPRai](#crisprai) |
|
| 22 |
+ - [Cas12a methods](#cas12a-methods) |
|
| 23 |
+ - [DeepCpf1 score](#deepcpf1-score) |
|
| 24 |
+ - [enPAM+GB score](#enpamgb-score) |
|
| 25 |
+ - [Cas13d methods](#cas13d-methods) |
|
| 26 |
+ - [CasRxRF](#casrxrf) |
|
| 27 |
+- [Off-target specificity scores](#off-target-specificity-scores) |
|
| 28 |
+ - [MIT score](#mit-score) |
|
| 29 |
+ - [CFD score](#cfd-score) |
|
| 30 |
+- [Indel prediction score](#indel-prediction-score) |
|
| 31 |
+ - [Lindel score (Cas9)](#lindel-score-cas9) |
|
| 32 |
+- [License](#license) |
|
| 33 |
+- [Reproducibility](#reproducibility) |
|
| 34 |
+- [References](#references) |
|
| 35 |
+ |
|
| 4 | 36 |
Authors: Jean-Philippe Fortin, Aaron Lun, Luke Hoberecht |
| 5 | 37 |
|
| 6 | 38 |
Date: July 1, 2022 |
| ... | ... |
@@ -550,6 +582,16 @@ input <- paste0(flank5, spacer, pam, flank3) |
| 550 | 582 |
results <- getLindelScores(input) |
| 551 | 583 |
``` |
| 552 | 584 |
|
| 585 |
+# License |
|
| 586 |
+ |
|
| 587 |
+The project as a whole is covered by the MIT license. The code for all |
|
| 588 |
+underlying Python packages, with their original licenses, can be found |
|
| 589 |
+in `inst/python`. We made sure that all licenses are compatible with the |
|
| 590 |
+MIT license and to indicate changes that we have made to the original |
|
| 591 |
+code. |
|
| 592 |
+ |
|
| 593 |
+# Reproducibility |
|
| 594 |
+ |
|
| 553 | 595 |
``` r |
| 554 | 596 |
sessionInfo() |
| 555 | 597 |
``` |
| ... | ... |
@@ -527,9 +527,20 @@ input <- paste0(flank5, spacer, pam, flank3) |
| 527 | 527 |
results <- getLindelScores(input) |
| 528 | 528 |
``` |
| 529 | 529 |
|
| 530 |
+ |
|
| 531 |
+# License |
|
| 532 |
+ |
|
| 533 |
+The project as a whole is covered by the MIT license. The code for all |
|
| 534 |
+underlying Python packages, with their original licenses, can be found in |
|
| 535 |
+`inst/python`. We made sure that all licenses are compatible with the MIT |
|
| 536 |
+license and to indicate changes that we have made to the original code. |
|
| 537 |
+ |
|
| 538 |
+# Reproducibility |
|
| 539 |
+ |
|
| 530 | 540 |
```{r}
|
| 531 | 541 |
sessionInfo() |
| 532 | 542 |
``` |
| 533 | 543 |
|
| 544 |
+ |
|
| 534 | 545 |
# References |
| 535 | 546 |
|
