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JetBrains-Research
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jbr
JBR Genome Browser
https://doi.org/10.1093/bioinformatics/btab376
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Add special support for RNA-Seq BAM files
#234
iromeo
opened
1 year ago
0
Bigwig - show name of values adjustment in detailed view, e.g. if `log` is used
#233
iromeo
closed
1 year ago
0
Do not show standard BED fields that are not covered by BED format in detailed cursor info
#232
iromeo
closed
1 year ago
0
Mention explicitly that position is 0-based in cursor info detailed dialog
#231
iromeo
opened
1 year ago
0
Use unique transcript id as a title of gene info dialog
#230
iromeo
closed
1 year ago
0
java.lang.IllegalArgumentException: screen X 804 coordinate out of range [0, 791)
#229
iromeo
closed
1 year ago
1
Load from ENCODE dialog hangs
#228
iromeo
closed
1 year ago
0
Adapt aux information according to the window size
#227
olegs
closed
1 year ago
0
Better size for information under cursor dialog
#226
iromeo
closed
1 year ago
0
ERROR TrackViewRenderComponent Prepare scales: FA05_hg38_pe.bam.filtered_dmr2337.v2.sam.bam.sorted.bam: [FAILED] after 24.16 ms
#225
iromeo
closed
1 year ago
0
Cannot invoke "htsjdk.samtools.SAMRecord.getAlignmentStart()" because "mate" is null
#224
iromeo
closed
1 year ago
0
NPE in GeneShelf.getGeneFromPoint(GenesTrackView.kt:644)
#223
iromeo
closed
1 year ago
0
Cursor lines stay after cursor is disabled
#222
Xewar313
closed
1 year ago
2
Save screenshots into clipboard
#221
iromeo
closed
1 year ago
0
Allow BAM track to be 20px height.
#220
iromeo
closed
1 year ago
0
RenderingKey(id=TRACK_DATA) not initialized on SessionOpen+Mouse Move
#219
iromeo
closed
1 year ago
1
Detailed info at mouse pointer dialog doesn't support closing by `ESC` press
#218
iromeo
closed
1 year ago
1
The wrong nucleotide is shown on mouse pointer for 'C' mismatch
#217
iromeo
closed
1 year ago
0
Enhance context menu behavior for multiple tracks selection if track has different value of some shared key
#216
iromeo
closed
1 year ago
1
Implement track info at cursor for basic track types
#215
iromeo
closed
1 year ago
3
Improve Information at position for bam track: show coverage + information about mismatches + methylation
#214
iromeo
closed
1 year ago
1
Allow to setup exact screenshot
#213
olegs
closed
9 months ago
2
Update TrackView detailed info at cursor dialog component
#212
iromeo
closed
1 year ago
0
Calculate info at cursor in background thread
#211
iromeo
opened
1 year ago
2
Add posibility to "append" session to open tracks instead of closing current session
#210
olegs
closed
1 year ago
0
Make methylation look different from other mismatches on small scale
#209
iromeo
closed
1 year ago
2
Fix Track context menu related dialogs position
#208
iromeo
closed
1 year ago
1
On track selection JBR always repains all tracks
#207
iromeo
opened
1 year ago
0
Add tooltip information when hovering over tracks
#206
Xewar313
closed
1 year ago
2
Add handling for bisulfite mismatches in BAM tracks
#205
Xewar313
closed
1 year ago
0
Improve BAM selection window
#204
Xewar313
closed
1 year ago
1
Recent BAM files are shown in recent session dialogs
#203
iromeo
closed
1 year ago
0
Remove direct dependency of BAM plugin on htsjdk
#202
Xewar313
closed
1 year ago
0
Show fraction of mismatches in BAM coverage bar
#201
Xewar313
closed
1 year ago
1
Add scale to BAM file coverage track
#200
Xewar313
closed
1 year ago
1
Calculate bam coverage using Fragments, not reads in PE libraries
#199
iromeo
closed
1 year ago
1
Support BAM files created using GRCh* chromosomes names
#198
iromeo
closed
1 year ago
2
UncheckedIOException: Error loading chrY from ~/.jbr_browser/genomes/hg38/hg38.2bit
#197
iromeo
closed
1 year ago
1
Axis ticks can be improved
#196
olegs
closed
1 year ago
0
Don't show multiple ticks in axis with same text
#195
olegs
closed
1 year ago
1
Session: Make session specific settings
#194
iromeo
opened
1 year ago
0
BAM: Hide reads detailed info, show only coverage
#193
iromeo
closed
1 year ago
1
BAM: Compact reads viewing mode
#192
iromeo
closed
1 year ago
1
Failed to create arithmetic track view
#191
olegs
opened
1 year ago
1
CGI track that could be enabled from 'View' menu could be used with overlap/jaccard function
#190
iromeo
closed
1 year ago
0
Consider adding mm39 genome reference to the JBR package
#189
olegs
closed
2 days ago
0
Tracks Overlap: SIMD optimization is not available for Apple Silicone
#188
iromeo
opened
1 year ago
1
Initial Bam Support
#187
iromeo
closed
1 year ago
0
New BED colouring option for scores that are pvalues
#186
iromeo
opened
1 year ago
1
Autoscale doesn't work with log2 transformation
#185
olegs
closed
1 year ago
0
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