d885db4b3623b749dd2aab366f979715 *DESCRIPTION
109ae992724a79fc818e06a328a12654 *NAMESPACE
abae0b1b4d0b2391a0a23892239b9af1 *NEWS.md
39f7b70084e865e70e1cf52109915283 *R/00-setup_data.R
e1a9ba316122a39dd2cf303f5577839e *R/01-qc.R
03f70a7aacf4d961df2fba0e8ba4b1d0 *R/02-gimap_filter.R
3bb0a7049102f8649825f38989439021 *R/03-annotate.R
e94c5b8068b5bced7f10db1db2fb81f9 *R/04-normalize.R
b16331ce557282af37d80bcbf92dab52 *R/05-calculate_gi.R
1ae33fc5cdcbac888c6964ab66b7fd5d *R/plots-gi.R
6c93c4eeb94204c457750199d6cb23a3 *R/plots-norm.R
93eb9eb0eb78ac8786859cb13dc77c0a *R/plots-qc.R
4cbaadf3ee9b3c12a21d610f10a47643 *R/utils.R
5dd2fa7d707c5e08cbfc6b52005f6f9e *README.md
a64062e56421adc68894e16fbff74427 *build/vignette.rds
3808c71e8dbeced6273fd559d88f7e09 *inst/doc/quick-start.R
5bb5c870784a63ff4a2ae49e56301338 *inst/doc/quick-start.Rmd
3078300ef9319f63934298a09b5bdf59 *inst/doc/quick-start.html
7f97e9794975fb3831446e2901fa856b *inst/doc/timepoint-example.R
4f88c9b01d90422525e16d043a71d7b5 *inst/doc/timepoint-example.Rmd
d2f0c05dea2eca9ad06948f42d427137 *inst/doc/timepoint-example.html
6b135dc5c5e21004e500c154383044a5 *inst/doc/treatment_example.R
10b12ca856554a8676991f15870aeef5 *inst/doc/treatment_example.Rmd
ac6ccae004e9a199b329ec007884db4e *inst/doc/treatment_example.html
1f095225128d10f2cc91610114cd24ff *inst/example_qc_report.Rmd
9e25401fd1a0b0aac0115efba2565bf5 *inst/example_qc_report.html
ab80f0d09d49a6a289d0798dc5178fc5 *inst/extdata/Achilles_common_essentials.csv
e8b79941a3dbe81de0aa14897f97f463 *inst/extdata/creds/encrypt_pass.rds
57a844fd64959ccf7112b119730dad91 *inst/extdata/creds/figshare_creds.rds
33bf3105ea36a8650b28913310f2913b *inst/extdata/creds/figshare_encrypt.rds
1f095225128d10f2cc91610114cd24ff *inst/extdata/gimapQCTemplate.Rmd
7842dbf07f9edca0b78b731bf743b9eb *inst/extdata/pgPEN_annotations.txt
a2f93f45eae729474d6d83003e4fa0e5 *inst/extdata/pgRNA_ID_pgPEN_library_comp.csv
14fd1238c49e862b26e03229e6b9f89e *man/calc_gi.Rd
46b05340deed17257e5ee7450b11c347 *man/check_internet_available.Rd
efb662da4b92d990395f634750ea1252 *man/cn_setup.Rd
176c778f0fff063b2a8df847796865da *man/ctrl_genes.Rd
be97e2b3350b37b1660184f98723edbf *man/delete_annotation.Rd
ad32b636b51cba0fcb194e9596024870 *man/delete_example_data.Rd
6613acd88fae875e5758d2fd4fe743d5 *man/encrypt_creds_path.Rd
ca279baa32d13480a21bee07a5129360 *man/example_data_folder.Rd
5be4d2b9e05d3131d7be438b0cef548d *man/get_example_data.Rd
33eae752c839be3ddd71511e337f316a *man/get_figshare.Rd
c82865022458c91c35a60455af3d7fb4 *man/gimap_annotate.Rd
3295c26b0446b8429197a7863d7d839d *man/gimap_filter.Rd
7001a85a3d10def1ca7d72d272ede714 *man/gimap_normalize.Rd
e6c87c81876f60d6e903176ae9ab202c *man/gimap_object.Rd
0ef5dc2d246892e97a99496ff30e2150 *man/gimap_stats.Rd
3e31f2fcbb4f6690739a80dadcb65ef3 *man/key_encrypt_creds_path.Rd
f0462616001a6ffe7bdab2dd8babe820 *man/pipe.Rd
ed2e6b38bc5431b056f243fd11e24034 *man/plot_crispr.Rd
3755ce27ddb364e5c5023a26e297c8ca *man/plot_exp_v_obs_scatter.Rd
94060305a11c04a6740c9f424d455a20 *man/plot_rank_scatter.Rd
8f2dc5c2aba200869595d0e506c1984b *man/plot_targets.Rd
a29761286ab7a039ee29ffb29d4ef96f *man/plot_theme.Rd
6c7562105beace7a30ff6d67c5514fe4 *man/plot_volcano.Rd
48c3925336f0ab75f5c0fdf46f84672f *man/qc_cdf.Rd
2a8f89d836562759653bd80ec2d4f068 *man/qc_constructs_countzero_bar.Rd
fc831f29842e50d42c7a6d8a703d6b6f *man/qc_cor_heatmap.Rd
ebd0c2b032a4e41431b3b466284c83c1 *man/qc_filter_plasmid.Rd
3daa8dfb60c7f8bf76ba3cf4c384dbff *man/qc_filter_zerocounts.Rd
f6b9ad1c0c65d1e76a37ca742b5b3bad *man/qc_plasmid_histogram.Rd
db4aacf41e27202daf2d6e67d7e8646d *man/qc_sample_hist.Rd
325e92e1bbf3ad08427e87f0bf0e5ff2 *man/qc_variance_hist.Rd
948ca6f46218a3645cb6650975f7cd4a *man/run_qc.Rd
f74459bc92e421e85f8d0e8d14f2bc81 *man/save_example_timepoint_data.Rd
2d479d3236600057c0e368019bf706a2 *man/save_example_treatment_data.Rd
da1440f8952fac17af6257cba45603e2 *man/setup_data.Rd
51755fa86e567b2786868dafc448c6ea *man/supported_cell_lines.Rd
237f9abec4994b15544a3f94c3339a39 *man/tpm_setup.Rd
b3d2e8791ddaba0ac94191361a336be9 *tests/testthat.R
bef5b1072aaf59687e53cee60893a8db *tests/testthat/helper-skip.R
e791a4a20a6465db85aed77c8e177509 *tests/testthat/test-annotate.R
7be4a163cb33e9c095a4b5bc9def7395 *tests/testthat/test-figshare.R
b99579e4080b8fb9f6c897f7d5a6ff90 *tests/testthat/test-gi-calc.R
a8a6ddcd8a211a4d0590d2d750b4a9db *tests/testthat/test-normalize.R
e16084415d53123e90f3a78ba41fa550 *tests/testthat/test-run_qc.R
e36fe5ccebfd51503717ad1a964ddae9 *tests/testthat/test-setup_data.R
6bee842fd3149c165c79750c7d00f7a0 *vignettes/images/results_table.png
d0431667829a2dc53ed83504f4bc6f93 *vignettes/images/volcano_plot.png
8063316bbead73484ba0d73b6ac98d50 *vignettes/output_timepoints/CNOT8_CNOT7.png
1f095225128d10f2cc91610114cd24ff *vignettes/output_timepoints/example_qc_report.Rmd
a670ebf6dbbb35e7cb27ebb838a9414d *vignettes/output_timepoints/example_qc_report.html
fc16c02a2def8d3e2551e3f9670d8378 *vignettes/output_timepoints/exp_v_obs_scatter.png
3a26b130b58f50766e9f3e31cf098594 *vignettes/output_timepoints/plot_rank_scatter.png
a98d4c09e55e97b3e59404e0aa76cd4b *vignettes/output_timepoints/volcano_plot.png
097cc36c9890c9009edf00fc09608aec *vignettes/output_treatment/DUSP21_DUSP18.png
93e0be9402b84b1d42c060df85a29151 *vignettes/output_treatment/NDEL1_NDE1.png
4dc5fa8a0907230b86098f2c520b1a8e *vignettes/output_treatment/exp_v_obs_scatter.png
02ea4b445a2c3cf7c0b72d8c198b8023 *vignettes/output_treatment/gi_scores.tsv
ec1895f349c937b3b3d5b9caf26e5348 *vignettes/output_treatment/plot_rank_scatter.png
646d6998fdd533695ebb2a709cbf37be *vignettes/output_treatment/plot_volcano.png
5bb5c870784a63ff4a2ae49e56301338 *vignettes/quick-start.Rmd
4f88c9b01d90422525e16d043a71d7b5 *vignettes/timepoint-example.Rmd
10b12ca856554a8676991f15870aeef5 *vignettes/treatment_example.Rmd
