Commits · c4cce888f5658e4a8cc21ef48af05bd63c134287 · loosolab / software / multicrispr · GitLab

01 Nov, 2019 1 commit
- @import -> :: · c4cce888
  aditya.bhagwat authored Oct 31, 2019
  
  c4cce888
31 Oct, 2019 4 commits
- Comply with BioC 80:50:4 (width:length:tab) · 8c405bd0
  aditya.bhagwat authored Oct 31, 2019
  
  8c405bd0
- (temporarily) remove [vw]ignettes · 11e2ff76
  aditya.bhagwat authored Oct 31, 2019
  
  11e2ff76
- Remove obsolete lines from DESCRIPTION · fb088574
  aditya.bhagwat authored Oct 31, 2019
  
  fb088574
- Fix score_cas9s and find_cas9s (cont'd) · 70f35f7e
  aditya.bhagwat authored Oct 31, 2019
  
  70f35f7e
29 Oct, 2019 1 commit
- Complete filter_no_offtargets and filter_doench_score · bf63f579
  aditya.bhagwat authored Oct 29, 2019
  
  bf63f579
28 Oct, 2019 6 commits
- (1) Import seqlengths from GenomeInfoDb. (2) Discontinue get_bsgenome and... · f2766d47
  aditya.bhagwat authored Oct 28, 2019
```
(1) Import seqlengths from GenomeInfoDb. (2) Discontinue get_bsgenome and require explicit BSgenome specification. (3) Ensure proper :: assertive import.
```
  f2766d47
- Rename db -> txdb (to disambiguate from orgdb) · a0e9f304
  aditya.bhagwat authored Oct 28, 2019
  
  a0e9f304
- Add assertive to DESCRIPTION, but rm it from imports.R (had done the opposite) · c0ef7f94
  aditya.bhagwat authored Oct 28, 2019
  
  c0ef7f94
- (1) bed_to_granges, seqs: now BSgenome-based (2) granges -> gr. (3) Update... · f938112b
  aditya.bhagwat authored Oct 28, 2019
```
(1) bed_to_granges, seqs: now BSgenome-based (2) granges -> gr. (3) Update imports.R , NAMESPACE, and man/
```
  f938112b
- Move offtargetanalysis functions to separate file · 25f37019
  aditya.bhagwat authored Oct 28, 2019
  
  25f37019
- @import assertive -> assertive:: · 046765bb
  aditya.bhagwat authored Oct 28, 2019
  
  046765bb
23 Oct, 2019 6 commits
- plot_karyogram: add . <- NULL to satisfy check · fde29f85
  aditya.bhagwat authored Oct 23, 2019
  
  fde29f85
- COMBINE bed_to_granges.R, genes_to_granges.R => xxx_to_granges.R · 6260812b
  aditya.bhagwat authored Oct 23, 2019
  
  6260812b
- @importFrom GenomeInfoDb seqlevels, seqlevelsInUse, seqlevelsStyle · 96f04afd
  aditya.bhagwat authored Oct 23, 2019
  
  96f04afd
- Enhance plot_karyogram: ensure stable chromosome order · ad98219d
  aditya.bhagwat authored Oct 23, 2019
  
  ad98219d
- DEVELOP genes_to_granges, genefile_to_granges, and annotate_granges · 069531de
  aditya.bhagwat authored Oct 23, 2019
  
  069531de
- RENAME read_bed -> bed_to_granges · 90f8a13b
  aditya.bhagwat authored Oct 23, 2019
  
  90f8a13b
22 Oct, 2019 8 commits
- Add example to EnsDb.Mmusculus.v98() and EnsDb.Hsapiens.v98() · b267c4b9
  aditya.bhagwat authored Oct 22, 2019
  
  b267c4b9
- Ensure functions <= 50 lines to satisfy BiocCheck · 36eaf738
  aditya.bhagwat authored Oct 22, 2019
  
  36eaf738
- Ensure 80-character lines to satisfy BiocCheck · 0f32db11
  aditya.bhagwat authored Oct 22, 2019
  
  0f32db11
- Ensure 4-space indentation to satisfy BiocCheck · a436d599
  aditya.bhagwat authored Oct 22, 2019
  
  a436d599
- Rm obsolete code · 373ff59c
  aditya.bhagwat authored Oct 22, 2019
  
  373ff59c
- Ensure 4-space indentation to satisfy BiocCheck · 97462443
  aditya.bhagwat authored Oct 22, 2019
  
  97462443
- Add missing require(magrittr) in example · a883d670
  aditya.bhagwat authored Oct 22, 2019
  
  a883d670
- Accomodate extend_fourways -> extend · 64d6ea5d
  aditya.bhagwat authored Oct 22, 2019
  
  64d6ea5d
21 Oct, 2019 14 commits
- Accomodate renaming: find_cas9ranges -> find_cas9s · 8644881b
  aditya.bhagwat authored Oct 21, 2019
  
  8644881b
- double_flank -> flank_fourways · 70f0f053
  aditya.bhagwat authored Oct 21, 2019
  
  70f0f053
- Rename: complement -> add_inverse_strand (returns both original AND complementary strand) · b23689ed
  aditya.bhagwat authored Oct 21, 2019
  
  b23689ed
- Fix annotate_granges example · d7ee0209
  aditya.bhagwat authored Oct 21, 2019
  
  d7ee0209
- GenomeInfoDb: @import -> :: · 70f5aa7f
  aditya.bhagwat authored Oct 21, 2019
  
  70f5aa7f
- txdb, ensdb -> db · c367ca09
  aditya.bhagwat authored Oct 21, 2019
  
  c367ca09
- Biostrings, GenomeInfoDb: @import -> :: · 0463f8b8
  aditya.bhagwat authored Oct 21, 2019
  
  0463f8b8
- Update vignette · 276dcac6
  aditya.bhagwat authored Oct 21, 2019
  
  276dcac6
- Update test_slop to accomodate renaming of slop() -> extend() · 2b26c0ad
  aditya.bhagwat authored Oct 21, 2019
  
  2b26c0ad
- document() · b8a95376
  aditya.bhagwat authored Oct 21, 2019
  
  b8a95376
- ADD inst/scripts/annotationhub_resources.R · a9d56c5a
  aditya.bhagwat authored Oct 21, 2019
  
  a9d56c5a
- find_cas9s: accomodate renaming of (canonical)chromosomes -> (canonical)seqlevels · 3dcc11f9
  aditya.bhagwat authored Oct 21, 2019
  
  3dcc11f9
- find_cas9s: accomodate renaming of slop_fourways -> extend_fourways · 04f16cb4
  aditya.bhagwat authored Oct 21, 2019
  
  04f16cb4
- Update find_cas9s arguments: targetranges -> gr, add inclcompl · f014edfc
  aditya.bhagwat authored Oct 21, 2019
  
  f014edfc