de3a38901f168bab95bc1426eca70b5d *DESCRIPTION
c846827d786fa7024adbe3356c2b33bd *NAMESPACE
9e09fda7a0e87036b3d265a5e870bb73 *NEWS
3a142421d1b69971ae1f50214ef43621 *R/bam_handler.R
aea5ae2939d73e048a425f6088decb55 *R/coverage_operations.R
9fd7c816374805b50331e61b402705d3 *R/demo.R
015e0b3cf7c65cf74373327d6615d970 *R/heatmap_from_metagene.R
eccaab31920f4fc170bfdf5c5020f45a *R/metagene.R
67dd3c08177b5c8247beddf1079c5d94 *R/normalization.R
96ec8cc98082902c83d304f6e88d80a3 *R/parallel_job.R
5e8953c7bef51be4ff7efee6442ecb4e *R/parameter_manager.R
7c19f08d90cd72ad97fda8a12cc713e7 *R/permutation.R
f7229fa13cebf047c5a5277aff95c61f *R/plot_metagene.R
f8eea93e36aeaefe9929ef6871e2cb39 *R/validations.R
d6f58cf83002444ad5c23d94c8888d3b *README.md
9886067c3894a9d43495853e9f61454b *build/vignette.rds
f3b09492171461d56be8d60f9f2eac07 *inst/doc/metagene2.R
682077e2beaa31eb7a7c726404e6b477 *inst/doc/metagene2.Rmd
f6e52bb589d2e23d5528896e3ff82899 *inst/doc/metagene2.html
78d967af5a72e9852b5ba09dff85577d *inst/extdata/DPM1.bed
f16e52df5fa3297e389dbee0b9030e52 *inst/extdata/DPM1less.bed
db6fede445f08973d61661bc73ffcf32 *inst/extdata/NDUFAB1.bed
28e72f299ac7c3e9ce1816f093d5deb8 *inst/extdata/NDUFAB1less.bed
4d088a4138d371f77a73b8cc33afb33c *inst/extdata/align1_rep1.bam
d79bac7839a0883d8ca416e12f84b73d *inst/extdata/align1_rep1.bam.bai
52fb78065facdce583564de8e6124950 *inst/extdata/align1_rep1.bed
782a4be5a2893401f2fde0b286e09223 *inst/extdata/align1_rep2.bam
fa6b261ffddadbb728d9898f3cce5341 *inst/extdata/align1_rep2.bam.bai
be219f7888fa2e2241021faa8aaffa54 *inst/extdata/align2_rep1.bam
0b7000fe766a344b11fe02d8e9e5777c *inst/extdata/align2_rep1.bam.bai
0fc46ddd51756004208d9acd4463b3eb *inst/extdata/align2_rep2.bam
9ef0f9008ea3a5cbde4408d6b784a9f5 *inst/extdata/align2_rep2.bam.bai
5cbb647147807a1a53e1ec4b46dd810b *inst/extdata/coverage.bam
f9ee30019511c70b0d8ec32cdd8a222a *inst/extdata/coverage.bam.bai
7d3db9be2a04541b940f1ae0ff999f89 *inst/extdata/ctrl.bam
b30f560ba20c24ce7724ac670554118e *inst/extdata/ctrl.bam.bai
c20ef1ad63bd5096ceb67fe82a71869c *inst/extdata/ctrl.bed
c3e5d029c500581ad28e3fff2b4e402c *inst/extdata/cyto3.bam
edea434961af38c8ab2c07cf2d590272 *inst/extdata/cyto3.bam.bai
c3fae94379f7567e4b6791dd3748d51e *inst/extdata/design.txt
e67215097be4262d5b1740b0a6e2d5c5 *inst/extdata/different_header.bam
80c7b958206df0b9282fd28cdcf80f8b *inst/extdata/different_header.bam.bai
b12de80a823644d4593b595406f24462 *inst/extdata/fake_align1.bam
90894ce735b384bc47c399c9c7ef76c9 *inst/extdata/fake_align1.bam.bai
e15266ba92183ff7be16108fc818a9e8 *inst/extdata/fake_align1.sam.coverage.RData
b602b24867aed7390fefd72cace15b8a *inst/extdata/fake_align1.sam.coverage.df
c445c5d4a747a1ed8f2c428e8e8a6afd *inst/extdata/fake_align1.sam.coverage_rpm.RData
843d8439eb5519157dcef5f6d94d1849 *inst/extdata/fake_align1.sam.regions.RData
944fabc09420c374992e8b6cf56d800d *inst/extdata/fake_align1_minus.bam
a9264db08a52ed4de945ca2e786014de *inst/extdata/fake_align1_minus.bam.bai
3d8716461d6108e8ae6c75b32e5d5cfa *inst/extdata/fake_align2.bam
034116c64c34ee94f9f402f0f8c49b43 *inst/extdata/fake_align2.bam.bai
b6054e93725a6c6aa6eb791e553849b4 *inst/extdata/fake_align2.sam.coverage.RData
323f0d1155f54c47804b635b6c3f6a3a *inst/extdata/fake_align2.sam.coverage.df
c445c5d4a747a1ed8f2c428e8e8a6afd *inst/extdata/fake_align2.sam.coverage_rpm.RData
843d8439eb5519157dcef5f6d94d1849 *inst/extdata/fake_align2.sam.regions.RData
5f31bd153aca13fdcc68546337f32034 *inst/extdata/fake_align3.bam
1f92454a20dc52e187e4b76e1611e222 *inst/extdata/fake_align3.bam.bai
8120b024a25868435bbc111f9e68e939 *inst/extdata/fake_align3.sam.coverage.RData
dce0167a61889e04a7424ba68d739e32 *inst/extdata/fake_align3.sam.coverage.df
29d5263b7e7f56c2396197e904c69650 *inst/extdata/fake_align3.sam.coverage_rpm.RData
843d8439eb5519157dcef5f6d94d1849 *inst/extdata/fake_align3.sam.regions.RData
bf962dc74ed9276347b3cd6ce8b0bea3 *inst/extdata/list1.bed
5de7ad021b01089b0f5d87b7497dfb5b *inst/extdata/list1.broadPeak
bb671659a19d842a15dd78d92db812df *inst/extdata/list1.narrowPeak
3736b486aafc64f19de131f52c914572 *inst/extdata/list1.txt
388f100d385fbc338a4f5cbdd963cded *inst/extdata/list2.bed
d69dfbed24e342d9ed9178b0b8eb2bc7 *inst/extdata/list2.txt
268913b0f7218ffb4299da3f642802ef *inst/extdata/list_coverage.bed
136ea4d6a8ece210471622bad1ea36ba *inst/extdata/lists.bed
b12de80a823644d4593b595406f24462 *inst/extdata/not_indexed.bam
158432757cc4142bbaa9d9ad5ecb9ff5 *inst/extdata/nuc3.bam
3afa0f0a6339b1a96d4305f925394241 *inst/extdata/nuc3.bam.bai
ee1b78a4562c664cf0e41d8b18e48afe *inst/extdata/test.gff
2103cbbaa15bf58cb3a8c7f15d1efd31 *inst/extdata/test.gtf
52e6ffe2438cb4cc49cd42c44d8d0f44 *inst/unitTests/Makefile
c03ddb21d77c2b4152daaa12c14227b0 *inst/unitTests/test_bam_handler.R
50c6b4c2857215c3dd9a2367f621e703 *inst/unitTests/test_demo.R
ccbee1f7b94806a3919397d69b7f7005 *inst/unitTests/test_heatmap.R
b96a5481ec9a7fe66db62b71ba7ee11d *inst/unitTests/test_metagene.R
dca6cfbba2164aa51fec600cab7be2b9 *inst/unitTests/test_parallel_job.R
84c18f0ebc7791f3460fb6d9c5172cc8 *inst/unitTests/test_parameter_manager.R
9f74a005ca47488d8ce6fb7cc33dd5cc *man/Bam_Handler.Rd
17b22884e35529b9071aa8457afe7588 *man/as_is_region_order.Rd
69cde7f9d67102a211754c8fe21b8cbe *man/coverage_order.Rd
57b807c520f404c2bac8f89bce196019 *man/get_demo_bam_files.Rd
84d6a0c01b731036581f395329c36fb0 *man/get_demo_design.Rd
370ca0691bf82b48115dc72c605bec39 *man/get_demo_metagene.Rd
b3294c1e5e3e2c61ffdbc98b84bbdcdd *man/get_demo_region_filenames.Rd
adbcd3fc1d0282e7094df53a90bc47cd *man/get_demo_regions.Rd
e34e03cd8d765bacbae0f03627cfb010 *man/get_demo_rna_bam_files.Rd
cac9ce6e0e666ec2e05bfc5fdff0685b *man/get_demo_rna_regions.Rd
81b03261cfcf0b73f8f1864b26038916 *man/metagene2.Rd
c0fe2675ce02b583a1bf9a7077f623f8 *man/metagene2_heatmap.Rd
f456cbb5949cbfa0d3aa7f49106833fd *man/plot_metagene.Rd
75f380949f6f58a7c08afcfeda5d65bd *tests/runTests.R
2c5bf9e74c4654787527ccb60a789887 *vignettes/img/processing_step_schema.png
682077e2beaa31eb7a7c726404e6b477 *vignettes/metagene2.Rmd
