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GoekeLab
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bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
GNU General Public License v3.0
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can you guys make bambu run on command line
#398
yuukiiwa
opened
11 months ago
0
Isofrom quantification Error: median(): detected NaN
#397
TingQi2020
closed
11 months ago
0
bambu command not recognized
#396
dvirdi01
closed
11 months ago
4
Incomplete result from minimap2-aligned bam files
#395
zhangkn3
closed
11 months ago
19
The deprecated feature was likely used in the bambu package
#394
alexander-schl
closed
1 year ago
3
Discrepancy gene counts (bambu) with less and more sequencing depth
#393
NikoLichi
closed
11 months ago
6
Including bambu annotation/GRanges for DEXSeq
#391
rugilemat
closed
11 months ago
1
Request: Provide a container
#390
andreas-wilm
closed
1 year ago
2
Don't compress gene assignments before fusion assignment
#389
andredsim
opened
1 year ago
1
Fix crash when no warnings from bam
#388
andredsim
closed
1 year ago
1
Subsetting annotation for protein_coding biotypes
#387
kenneditodd
closed
11 months ago
2
Update XGboost models for new version
#386
andredsim
opened
1 year ago
1
Failed to find a rowRanges() method for CompressedGRangesList objects.
#385
alexyfyf
closed
1 year ago
4
Bug fix plot bambu
#384
cying111
opened
1 year ago
1
plotPCA variance explained disagree with prcomp and factoextra pacakge
#383
NikoLichi
closed
10 months ago
1
Question: Could there be any difference in the output when the "lowMemory" is set to True in bambu?
#382
youyupei
closed
1 year ago
2
question:features used for junction correction.
#381
HongYhong
closed
1 year ago
2
dplyr 1.1.0. The deprecated feature was likely used in the bambu package. Warning message
#380
Michael-m6A
opened
1 year ago
3
Definition/threshold for full-length counts reported by Bambu
#378
bernardo-heberle
closed
1 year ago
0
Error in names(warnings) <- sampleNames : 'names' attribute [1] must be the same length as the vector [0]
#377
msagniez
closed
1 year ago
6
Update citation link in readme
#376
cying111
closed
1 year ago
0
Error with constructedAnnotations
#374
kainth-amoldeep
closed
11 months ago
2
include documentation for fusion mode
#373
cying111
opened
1 year ago
1
reduce memory and speed up assignGeneId from issue #368
#372
andredsim
closed
1 year ago
1
Fix single exon read class multiple assignment bug
#371
andredsim
closed
1 year ago
1
Question about using yieldSize and ncore parameters together
#370
bernardo-heberle
closed
1 year ago
2
Performing transcript discovery for multiple tissue types wiith Bambu
#369
bernardo-heberle
closed
1 year ago
2
Error in Assigning Gene IDs to Unstranded Read Clusters
#368
HongYhong
closed
1 year ago
3
Add lowConfidence transcripts to output and improve NDR filtering options
#367
andredsim
opened
1 year ago
1
Small bug fix for Issue #364
#366
andredsim
closed
1 year ago
1
BiocParallel errors when using lowMemory = TRUE
#365
zhenLiuXplr
closed
1 year ago
2
Missing value error from checkFeatures
#364
ChangqingW
closed
1 year ago
5
Small Bambu changes and fixes
#363
andredsim
closed
1 year ago
1
Re-running quantification after filtering transcripts without unique or full-length support to improve quantification accuracy
#362
bernardo-heberle
closed
1 year ago
2
Following up BiocParallel errors in #340
#361
seongwoohan
closed
11 months ago
19
how to find relavent gene of incompatible aligned reads?
#360
icanccwhite
closed
11 months ago
7
Not working for UCSC fasta and annotation
#359
alexyfyf
opened
1 year ago
1
Non integer transcript counts
#358
rotem-a
closed
11 months ago
3
how to find the bambu assigned transcript of aligned reads
#357
icanccwhite
closed
1 year ago
6
Bambu discovers "new genes" on the same strand and overlapping known gene coordinates of given annotation
#356
bernardo-heberle
closed
1 year ago
2
bug fix
#355
cying111
closed
1 year ago
1
Gene counts underestimated and/or entirely inconsistent with IGV visualizations
#354
itslittman
closed
11 months ago
2
Issue with `writeBambuOutput`
#353
paulimer
closed
1 year ago
3
BiocParallel error detected NaN with emWithL1 during isoform quantification
#352
m-noonan
closed
1 year ago
2
error using bambu
#351
acarmas1
closed
1 year ago
1
How does Bambu handle quantification of "truncated" reads that map uniquely to a transcript?
#350
bernardo-heberle
closed
1 year ago
2
Questions regarding example in README.dm
#349
piechottam
closed
1 year ago
3
bug fix merge
#348
cying111
closed
1 year ago
0
Bug FIxes
#347
andredsim
closed
1 year ago
1
BiocParallel Error
#341
AJTDaedalus
closed
1 year ago
1
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