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rnabioco
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raer
Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments
https://rnabioco.github.io/raer/
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Cannot open URL 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_assembly_report.txt'
#121
shmmuzhangh
closed
3 months ago
3
Cannot connect to ExperimentHub server
#120
shmmuzhangh
closed
3 months ago
5
use txdbmaker package for makeTxDb... functions
#119
kriemo
closed
7 months ago
0
fix errors in ss2 reporting
#118
kriemo
closed
7 months ago
0
add support for DNAString/DNAstringSet
#117
kriemo
opened
7 months ago
0
fix R stack imbalance
#116
kriemo
closed
8 months ago
0
avoid possible memory issue when building index.
#115
kriemo
closed
10 months ago
0
create gh release matching bioc version
#114
jayhesselberth
closed
11 months ago
0
Bioc updates
#113
kriemo
closed
1 year ago
0
use tempdir() properly...
#112
kriemo
closed
1 year ago
0
handle false positive warning when expanding ranges
#111
kriemo
opened
1 year ago
0
Vignette and bioc updates
#110
kriemo
closed
1 year ago
1
Fix memory leaks reported by valgrind
#109
kriemo
closed
1 year ago
0
remove the output file options from pileup_sites()
#108
kriemo
closed
1 year ago
0
modularize
#107
kriemo
closed
1 year ago
0
drop genomic-unstranded option
#106
kriemo
closed
1 year ago
0
standardize fasta arg
#105
kriemo
closed
1 year ago
0
pkgdown error
#104
kriemo
closed
1 year ago
2
single cell AEI functionality
#103
kriemo
closed
1 year ago
0
Consensus base counting for pileup_cells
#102
kriemo
closed
1 year ago
0
allow pileup_cells to process multiple alleles per site
#101
kriemo
closed
1 year ago
0
additional utilities
#100
kriemo
closed
1 year ago
0
respect min_depth and min_variant_reads
#99
kriemo
closed
1 year ago
0
update vignette to use raerdata package
#98
kriemo
closed
1 year ago
0
implement calc_AEI method for droplet scRNA-seq data
#97
kriemo
closed
1 year ago
0
support BamFile and BamFileList classes as inputs
#96
kriemo
closed
1 year ago
0
updates for de related functions
#95
kriemo
closed
1 year ago
0
calc_aei improvements
#94
kriemo
closed
1 year ago
0
rework rownames to be consistent between pileup_cells and pileup_sites.
#93
kriemo
closed
1 year ago
0
update tests and catch some warnings
#92
kriemo
closed
1 year ago
0
Additional site statistics to examine strand-bias and confidence
#91
kriemo
closed
1 year ago
0
additional code clean up, tests, fixes for some bioc notes and warnings.
#90
kriemo
closed
1 year ago
0
Skip n bases
#89
kriemo
closed
1 year ago
0
rename main to devel
#88
kriemo
closed
1 year ago
1
Prune old code
#87
kriemo
closed
1 year ago
0
use region index approach and rename output columns from pileup_sites()
#86
kriemo
closed
1 year ago
0
pileup_cells(): add option to process smart-seq2 style libraries
#85
kriemo
closed
1 year ago
0
ref and alt naming of GR input for pileup_cells
#84
kriemo
closed
1 year ago
0
exclude multiallelics and other improvements
#83
kriemo
closed
1 year ago
0
functionality to examine expression of editing enzymes
#82
jayhesselberth
closed
1 year ago
1
find mispriming regions
#81
kriemo
closed
1 year ago
2
update vignette for new single-cell workflow
#80
jayhesselberth
closed
1 year ago
1
editing software categorization
#79
jayhesselberth
closed
1 year ago
2
use rse_adar_ifn in more examples
#78
jayhesselberth
closed
1 year ago
1
Create new GR annotation data for examples
#77
jayhesselberth
closed
1 year ago
0
Mark count_edits as internal
#76
jayhesselberth
closed
1 year ago
0
don't export `count_edits`
#75
jayhesselberth
closed
1 year ago
0
filter functions now provide feedback
#74
jayhesselberth
closed
1 year ago
1
Increase size of sample data
#73
jayhesselberth
closed
1 year ago
2
option to exclude reporting low frequency multiallelics
#72
kriemo
closed
1 year ago
0
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