Commits · 78f04e9d98797597366854fafaaaf8c6e2fa91d7 · loosolab / software / multicrispr

24 Dec, 2019 3 commits
- CHECK Fixes · 78f04e9d
  aditya.bhagwat authored Dec 24, 2019
  
  78f04e9d
- Unify interface of range arithmetic functions · 075b1a98
  aditya.bhagwat authored Dec 24, 2019
  
  075b1a98
- Complete find_pe_sites() · ecfd2383
  aditya.bhagwat authored Dec 18, 2019
  
  ecfd2383
12 Dec, 2019 1 commit
- Work on PE functionality · 0d23294c
  aditya.bhagwat authored Dec 12, 2019
  
  0d23294c
06 Dec, 2019 2 commits
- Add PE suppoort · a8d210d3
  aditya.bhagwat authored Dec 06, 2019
  
  a8d210d3
- Enhance plot_intervals(). Create up_flank(). Create down_flank() · ddd07232
  aditya.bhagwat authored Dec 06, 2019
  
  ddd07232
05 Dec, 2019 3 commits
- BiocCheck fixes · 9e433997
  aditya.bhagwat authored Dec 05, 2019
  
  9e433997
- plot_intervals: argumentify contig_var and n_head_tail · 611c22a9
  aditya.bhagwat authored Dec 05, 2019
  
  611c22a9
- Check & BiocCheck Fixes · adf11f64
  aditya.bhagwat authored Dec 04, 2019
  
  adf11f64
04 Dec, 2019 3 commits
- Rename R files · 5352dfbe
  aditya.bhagwat authored Dec 04, 2019
  
  5352dfbe
- Import most functions in BioC style (:: -> importFrom) · 19320f37
  aditya.bhagwat authored Dec 04, 2019
  
  19320f37
- Enhance plot_var: argumentify color_var · 72e9f457
  aditya.bhagwat authored Dec 04, 2019
  
  72e9f457
22 Nov, 2019 8 commits
- Generify variable names (cas9 -> crispr). Extend allowed mismatches from 2 to 4. · 33c62af8
  aditya.bhagwat authored Nov 22, 2019
  
  33c62af8
- Satisfy BiocCheck() · 605fb6bf
  aditya.bhagwat authored Nov 22, 2019
  
  605fb6bf
- vcountPDict(exclude = exclude_to_include('chr11')) · d404aa44
  aditya.bhagwat authored Nov 22, 2019
  
  d404aa44
- Rename: filter_no_offtarget -> filter_offtargetfree_sites · bf8e60a5
  aditya.bhagwat authored Nov 22, 2019
  
  bf8e60a5
- score_cas9s -> score_crispr_sites · 0cd8496a
  aditya.bhagwat authored Nov 22, 2019
  
  0cd8496a
- find_cas9s -> find_crispr_sites · 80fc5dc5
  aditya.bhagwat authored Nov 22, 2019
  
  80fc5dc5
- Check Fixes · 91c34e0c
  aditya.bhagwat authored Nov 22, 2019
  
  91c34e0c
- Export add_inverse_strand, improve identation, improve documentation · bb844185
  aditya.bhagwat authored Nov 22, 2019
  
  bb844185
11 Nov, 2019 1 commit
- Add R/09_alignment_offtargetanalysis.R · 28facf13
  aditya.bhagwat authored Nov 11, 2019
  
  28facf13
01 Nov, 2019 2 commits
- Complete vignette · 52396cfb
  aditya.bhagwat authored Nov 01, 2019
  
  52396cfb
- @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