2e1bf74f054cfbead283a2aa27ad89f2 *DESCRIPTION
83d50b57940c00275b58b68da3df97ef *NAMESPACE
5948339be83319acdfc8fd99ab552811 *NEWS.md
7155a2a38e896cdfa8fdcbd5d12e4166 *R/AlignmentBarchart.R
e9578cb0af6567f3d38a1b58c0b1b1bf *R/Crispr_Enrichment_test.R
c2f0fc2ac9c3b9d7fb3d563f712a0768 *R/DirTest.R
c9cb65bca8c4471b2a023797c05caa47 *R/GCbias.R
ffef1068a3b3ca28ebfd8e60868b43f3 *R/GenePvalsFromEset.R
8ab618a3658abe2e8e1ba9ee3d44ff2d *R/GeneratePRC.R
5dacefd23c2cb698f5cd410c4e6cd96e *R/GenerateROC.R
ce5b93bfda0ad6addfa07112c4f0b0a1 *R/GenerateSignalSummary.R
e1e1ceae503e2edcd1e49990ff3c5ec7 *R/GuideCDF.R
3c2b8d05346085246b1f31bd2397d597 *R/Normalization.R
df0821a153b20cbc0d1859471530dace *R/RRAalpha.R
8d9b72baf8aba0c2a3d081b110b80e4e *R/RankByRep.R
99cf71e36a018f9762554f57e295925b *R/Raw_read_densities.R
bd73d44e6c14d1547083c8e76aa20fc6 *R/StackedGuides.R
24a68b14e9be49406280bb7e90381d95 *R/ViewControls.R
504998bc3e81a5a9eccbfaf92c2a6fc1 *R/ViewGuides.R
e559400dd03d2372c91f80bca2e262a7 *R/ViewTopTargets.R
d5cd3a8550a357624924ab99291ce7a5 *R/annotations.R
38117fdcfe9a4f3a0f60858e7f250f2b *R/compareContrasts.R
d58520e2d17cb2310ff77c7758509dd4 *R/contrastScatter.R
5f9b152f8a30457ba27bc0303837d223 *R/discardTraceReads.R
42df91c6edce7b105fe4cac7101559e8 *R/fileutilities.R
38da3cd7fe796851e8b9aae516b8b6a6 *R/gCrisprTools.R
95e39dcd7cd2c59a658b4bf2a8ac104f *R/generateCAT.R
fd3bda9521ce7fde2abf802e7730d14e *R/generateReports.R
0c8cf238ba47b21ab03b20967bf33ece *R/processFit.R
ada28175048c9db152e0efca22eefe8d *R/sparrow_integration.R
ee57482244c35eeb64af08911fb8f956 *README.md
e55516d8b2e14c79793eddf0ed73ea19 *build/vignette.rds
11a8c01d9cc48da216c9379d020b2d5f *data/aln.RData
a7adbb6f21f3f9d3e4e035982aaa0981 *data/ann.RData
995786b5203efa3981ec5e4ec3cc1b3b *data/datalist
e75136ed2389f66e79f47e83fc5095f1 *data/es.RData
34187fd3ea1ff6576246cbec7f3d73ca *data/essential.genes.RData
3b0ed2bee8813c73cfa304cc9a7efaf4 *data/fit.RData
2c5a41c275f1728ae2c6a1c38cca1653 *data/resultsDF.RData
6d8a93d94536e8062ce6bd0a99c32ccc *data/se.RData
4d91604ff0aca55f5ee2abe34a8c7790 *inst/doc/Contrast_Comparisons.R
1756d82a0cd3d43af9c8697214b7c21f *inst/doc/Contrast_Comparisons.Rmd
327bb278f08279bebf427d3d529e3030 *inst/doc/Contrast_Comparisons.html
93fd67164de7970fc9e6d786941ee124 *inst/doc/Crispr_example_workflow.R
edc6a8d178a09e12251187da175fff2b *inst/doc/Crispr_example_workflow.Rmd
e24c8314adc513326adf1503a7f3d39e *inst/doc/Crispr_example_workflow.html
46feeb4a11084a6c7239bf5d61853b14 *inst/doc/gCrisprTools_Vignette.R
2285c0cf1bb4269a41865dcb8b3782f3 *inst/doc/gCrisprTools_Vignette.Rmd
05f95048d15b478f6f19ad3f13029a96 *inst/doc/gCrisprTools_Vignette.html
38649321f7e98325230bd397af19e063 *inst/rmarkdown/templates/CRISPR_QC_report/skeleton/skeleton.Rmd
38e8d3652cb0ece0ae905ffffc195681 *inst/rmarkdown/templates/CRISPR_QC_report/template.yaml
7c98c42d310301053cffd0f6c0607e4c *inst/rmarkdown/templates/CRISPR_contrast_report/skeleton/skeleton.Rmd
708272fe2e66f3d270af450537f6d44b *inst/rmarkdown/templates/CRISPR_contrast_report/template.yaml
7f3cf724d9cc51bcef6030c157c2e29c *inst/rmarkdown/templates/CRISPR_report/skeleton/skeleton.Rmd
aad14ed2461fc76dc2275215affab3ff *inst/rmarkdown/templates/CRISPR_report/template.yaml
f544f4fd54489d80c7f7306d05ef34ee *inst/unitTests/test.GenePvalsFromEset.R
daad0ac5db82fdde56f04cd29a3ad6b0 *inst/unitTests/test.RRAalpha.R
c8c6bd01538dd23928b2f2f4ad60bd9b *inst/unitTests/test.SE.R
43e196461a883b73851a85d0a94966a9 *inst/unitTests/test.roc.R
f6c2f095bde58bfe4bcb56483f88bb0c *man/aln.Rd
7f450c8f76867fb4282a15984354db96 *man/ann.Rd
4f918a101be17917f4bb74eeee1f33b8 *man/appendDateAndExt.Rd
68acec965f8011c9fc82769143ee7ff0 *man/ct.CAT.Rd
e8dc80d7bf8869df76d13519ffc499ad *man/ct.DirectionalTests.Rd
74ffe55fb8fa12eb5759e8f579cb4459 *man/ct.GCbias.Rd
454dea8f1968d13e30216ded1172f111 *man/ct.GREATdb.Rd
d3dcaa6e800573d9cfef586926b96279 *man/ct.PRC.Rd
1ae65c23cd29eab1bdeb928a35453c3e *man/ct.ROC.Rd
6531012f96e89bba19b0524a8a6b612e *man/ct.RRAaPvals.Rd
9f400ffaaaedcbc5d5cbc381a2420222 *man/ct.RRAalpha.Rd
1a34edf21a63191f84a94f0cae5afee1 *man/ct.RRAalphaBatch.Rd
66956241f3a3ce3aca58f5b0799709ae *man/ct.alignmentChart.Rd
d77a6f40734f7ccae347f2caab058327 *man/ct.alphaBeta.Rd
5101b6bbb0ffa59db734a3bdda11491e *man/ct.applyAlpha.Rd
05d662f9ba6d1f46649e7a9de8119ed3 *man/ct.buildSE.Rd
8464b9000b5ea49e147e29c12207225d *man/ct.compareContrasts.Rd
0aa7eb0ec4fdda5e1fc51d96c16ca62c *man/ct.contrastBarchart.Rd
b871ad910a74180b4f378f020ccd0606 *man/ct.drawColorLegend.Rd
0721375acd13c8b8e9c254369debf8ca *man/ct.drawFlat.Rd
b6df0df7d0759edd38438c05789ad3b6 *man/ct.ecdf.Rd
184587543d89a24ccb72f931bfc26653 *man/ct.expandAnnotation.Rd
b08ff52879e3b867ae0803ec20415f4b *man/ct.exprsColor.Rd
25a26f867f3d32888c6ecbfce1545c33 *man/ct.extractSE.Rd
3ba4e00b3e47b2571a19bd6982ef9048 *man/ct.filterReads.Rd
db599aa412447bffc936f5fe6d20fd69 *man/ct.gRNARankByReplicate.Rd
789332a8eb79ff11843974e4f24b73af *man/ct.generateResults.Rd
bdba09e6d34c84140965df0ac8a2dafc *man/ct.guideCDF.Rd
0552d17e079ff0aa6911c9ff090c6683 *man/ct.inputCheck.Rd
daaa55d1bd983c8a02993c6404b7c6eb *man/ct.keyCheck.Rd
8f626bc220bb02402c6f8a30cce87d92 *man/ct.makeContrastReport.Rd
40468d90fc344875d233ac84871670cd *man/ct.makeQCReport.Rd
a6e3e90604fac0c96ac34b5ec641cb49 *man/ct.makeReport.Rd
46e28e10b7c6d7d6310635ffb6cb297d *man/ct.makeRhoNull.Rd
f2f1eac588f68156c15956f6c93ab195 *man/ct.normalizeBySlope.Rd
4d28319dd4ae4c73cd1c2bb36636b355 *man/ct.normalizeFQ.Rd
9473bdeb9eb8e169c9cc258021de29d9 *man/ct.normalizeGenewise.Rd
cb77ace4c272fd374353469d0c9c912b *man/ct.normalizeGuides.Rd
fb6cea70c21809b7ebfc3955be4fe315 *man/ct.normalizeMedians.Rd
3be1ff2f2009eed0bbba203c59c97644 *man/ct.normalizeNTC.Rd
ef4e0902b95975d4518f104357a09d39 *man/ct.normalizeSpline.Rd
ddec2160acf1446a50e0e52b5d3f1db3 *man/ct.numcores.Rd
6b22cb28896900232e2f9f386d70bfc0 *man/ct.parseGeneSymbol.Rd
433a5919b5ee8529f3ea375fead56190 *man/ct.prepareAnnotation.Rd
b5d11727317e74bbbec902997e8f99b7 *man/ct.preprocessFit.Rd
0ecbb06d923315d28e8fce9bedbf3474 *man/ct.rankSimple.Rd
0c564977eb5f4e901fa41a2839348209 *man/ct.rawCountDensities.Rd
f8eafc0552d27b0251fabd61ec0df5d5 *man/ct.regularizeContrasts.Rd
6fb7c701d0b14183ccf7c077f1bb555d *man/ct.resultCheck.Rd
3609555c4d54e0a862ba680be30589cb *man/ct.scatter.Rd
3eff86316b2d1168e397f99a193fba57 *man/ct.seas.Rd
3b6e32985c406f273187b83a03413fa5 *man/ct.seasPrep.Rd
7104d92b211bff2adb76c8821acfff18 *man/ct.signalSummary.Rd
1228bb9e0653174bfbe46f8bfed63090 *man/ct.simpleResult.Rd
12e93d43603bf369f0f2f981427dea1f *man/ct.softLog.Rd
fca9d6654ea40190c53f0389032d0a49 *man/ct.stackGuides.Rd
f3170b74ff1420945bb807a42bd45922 *man/ct.targetSetEnrichment.Rd
9326523a354d5aa2947020fa3cf53f64 *man/ct.topTargets.Rd
eac97eaf99a5590276457adaadef4968 *man/ct.upSet.Rd
26372f0fdf0d0e71f46aaf8114a61d5b *man/ct.viewControls.Rd
40a314f1b18cbfc36cc2f08bc1b557c2 *man/ct.viewGuides.Rd
872fbfda6aa4dec2d2106f69938fd9fa *man/dir.writable.Rd
ad6c87ce546ae60f31095544bc990638 *man/es.Rd
6c6eee3971d7055487c94798f061a08c *man/essential.genes.Rd
607c41d638ab0221ccf3ef8f7840f2ea *man/fit.Rd
6957851123f1e5c2f250aa126d49c701 *man/gCrisprTools-package.Rd
f5232b58b44bfdf2bcfbd419dfdfddd8 *man/initOutDir.Rd
1d9760166453a190eb59b5ac0fcf2e93 *man/renderReport.Rd
103dba89a476cf29b792069f5a44df83 *man/resultsDF.Rd
e0caae4d3182d2356f22a521fbcce805 *man/se.Rd
b96e70c7bc77c859176d9c22d167fc0f *tests/unit.tests.R
1756d82a0cd3d43af9c8697214b7c21f *vignettes/Contrast_Comparisons.Rmd
edc6a8d178a09e12251187da175fff2b *vignettes/Crispr_example_workflow.Rmd
2285c0cf1bb4269a41865dcb8b3782f3 *vignettes/gCrisprTools_Vignette.Rmd
