thackl gggenomes issues

thackl / gggenomes

A grammar of graphics for comparative genomics

https://thackl.github.io/gggenomes/

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issues

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Find better way for x-axis than to overwrite `scale_x_continuous`

#54 thackl closed 3 years ago
0
Unable to import tutorial data

#53 mschecht closed 3 years ago
2
Text associated with overlapping gene regions

#52 jchariker closed 3 years ago
4
read_gff3 makes all features introns of ID tag is missing

#51 thackl closed 3 years ago
0
Added locate - like focus, but add loci as track instead of zoom; added position_* examples

#50 thackl closed 3 years ago
0
A filter_track() family might be quite useful after all

#49 thackl opened 3 years ago
0
Add life-cycle badges to function

#48 thackl closed 1 year ago
1
Default position for geom_feat should be "identity", or pile with "0" offset

#47 thackl closed 3 years ago
1
Add a function similar to focus but that just "hilights" new loci as features (no zoom)

#46 thackl closed 3 years ago
2
Made it possible to focus on several regions from the same parent sequence at once

#45 thackl closed 3 years ago
0
add_subfeats .transform="none" broken

#44 thackl closed 3 years ago
0
Last gggenomes example failed with mysterious error

#43 thackl closed 3 years ago
5
Update landing page example to match breaking changes

#42 thackl closed 3 years ago
0
make genes the first arguement of gggenomes for more intuitive usage. gggenomes() also reads files now

#41 thackl closed 3 years ago
0
Document all the geom's

#40 thackl opened 3 years ago
0
Improve docu for add_track functions

#39 thackl closed 3 years ago
0
various smaller fixes and improvements

#38 thackl closed 3 years ago
0
improve smart-read backend with new mapping of defined formats, extensions, context and parsers

#37 thackl closed 3 years ago
0
Test piping through non-R parsers (/exex/{gb2gff,seq-len}) on non-linux systems

#36 thackl opened 3 years ago
1
Reading gff3 with ##FASTA section broken

#35 thackl closed 3 years ago
0
write a help-topic on gggenomes table design and coordinate system

#34 thackl closed 3 years ago
1
harmonize different coordinate systems - gff 1[start,end] vs bed 0[start,end)

#33 thackl closed 3 years ago
0
Make intron coords consistently [1-based) the same way start/end are

#32 thackl closed 3 years ago
1
Check how non-coding geneish features like tRNAs, ncRNAs, are handle by geom_gene()

#31 thackl closed 3 years ago
0
parse key=value tags from fasta headers

#30 thackl closed 3 years ago
0
flip_nicely() failes on protein links

#29 thackl closed 3 years ago
0
Add gggenomes() usage doc/examples

#28 thackl closed 1 year ago
0
improve read docs and clean-up function reference

#27 thackl closed 3 years ago
0
Clean up text geoms and add gggenes fit label support

#26 thackl opened 3 years ago
0
Mark internal functions with @keywords internal to hide them from reference index

#25 thackl closed 3 years ago
0
Fix column width in @eval file_formats_rd() and add to def_names()/def_types()

#24 thackl closed 3 years ago
1
Add non-R parser scripts to exec/

#23 thackl closed 3 years ago
1
revamp landing page

#22 thackl closed 3 years ago
0
fix broken piling in isoforms

#21 thackl closed 3 years ago
0
Can I cite an alpha release version in my paper

#20 xvtyzn closed 3 years ago
2
piling isoforms broken in pkgdown examples

#19 thackl closed 3 years ago
1
improved pick api

#18 thackl closed 3 years ago
1
Support Methylation and ChIP-Seq data

#17 thackl opened 3 years ago
1
Example and maybe support for RNA-Seq data

#16 thackl opened 3 years ago
0
Support for SNP data - read_vcf, geom_snp

#15 thackl closed 1 year ago
1
Support for short and long read alignments - read _bam / geom_read

#14 thackl opened 3 years ago
0
Update landing page figure with new style

#13 thackl closed 3 years ago
1
Add read_alitv() to context-specific read_* functions

#12 thackl closed 3 years ago
5
Add a relocate()-like analog for pick(), maybe put()?

#11 thackl opened 3 years ago
0
make pick() work on bins not seqs

#10 thackl closed 3 years ago
0
fix for pick returns null

#9 thackl closed 3 years ago
0
pick() broken - returns NULL

#8 thackl closed 3 years ago
0
Add dependency for pkgdown

#7 iimog closed 3 years ago
0
Develop

#6 thackl closed 3 years ago
0
Read alitv

#5 iimog closed 4 years ago
0

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