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neurogenomics
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EpiCompare
Comparison, benchmarking & QC of epigenetic datasets
https://doi.org/doi:10.18129/B9.bioc.EpiCompare
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`rebin_peaks`: `Error in data.table::rbindlist(rebinned_peaks, use.names = TRUE, idcol = "assay") :
#103
bschilder
closed
2 years ago
5
Function overlap_percent report error unused arguments (peaklist1 = peaks, peaklist2 = reference_peak)
#102
Xindong-Sun
closed
2 years ago
2
Make `rebin_peaks` more efficient
#101
bschilder
closed
2 years ago
1
Error report when running the EpiCompare (github version, 0.99.21) with precision and recall curve
#100
Xindong-Sun
closed
1 year ago
1
Advertise docker container
#99
bschilder
closed
2 years ago
0
Address limitations of consensus peak calling
#98
bschilder
opened
2 years ago
0
Return paths to html files
#97
bschilder
closed
2 years ago
0
Fix file paths when reference >1
#96
bschilder
closed
2 years ago
0
Low precision-recall in example
#95
bschilder
closed
2 years ago
2
`compute_corr()`: Benchmark how bin sizes affect correlations
#94
bschilder
closed
2 years ago
1
Create consensus peaks
#93
bschilder
closed
2 years ago
1
Liftover causes extra weird chromosomes
#92
bschilder
closed
2 years ago
1
Check overlap_percent()
#91
serachoi1230
closed
1 year ago
0
Collapse code instead of removing entirely
#90
bschilder
closed
2 years ago
1
Enable mapping to/from mm9
#89
bschilder
closed
2 years ago
0
`Error in data.frame(seqnames = as.factor(seqnames(x)), start = start(x), : duplicate row.names: all`
#88
bschilder
closed
1 year ago
1
Bioc checks
#87
bschilder
closed
1 year ago
2
Open report after done generating
#86
bschilder
closed
2 years ago
0
Capture peak input URLs
#85
bschilder
opened
2 years ago
0
Add hex logo
#84
bschilder
closed
2 years ago
1
Enable filtering of peaks
#83
bschilder
closed
2 years ago
1
`overlap_percent`: Handle `length(peaklist2)>1`
#82
bschilder
closed
2 years ago
2
Add x/y axis label wrapping
#81
bschilder
opened
2 years ago
0
Add precision/recall plots
#80
bschilder
closed
2 years ago
5
`gather_files`: Annotate headers
#79
bschilder
closed
2 years ago
0
Required/ Suggested imports
#78
serachoi1230
closed
2 years ago
1
Save plot data
#77
bschilder
closed
1 year ago
3
`EpiCompare::EpiCompare`: return output file path(s)
#76
bschilder
closed
2 years ago
0
Standardise genome builds
#75
bschilder
closed
2 years ago
1
`plot_chromHMM`: sort X-axis
#74
bschilder
closed
2 years ago
0
Add timer to `EpiCompare::EpiCompare`
#73
bschilder
closed
2 years ago
0
Improve `EpiCompare` efficiency
#72
bschilder
closed
1 year ago
2
Handle `reference` with length >1
#71
bschilder
closed
2 years ago
3
Document genome builds of each built-in dataset
#70
bschilder
closed
2 years ago
0
Shorten code by setting names while making list
#69
bschilder
closed
2 years ago
0
Use "\code{}" instead of "``" in Roxygen notes
#68
bschilder
closed
2 years ago
0
Simplify loops
#67
bschilder
closed
2 years ago
2
Remove `S4Vectors` dep
#66
bschilder
closed
2 years ago
0
Replace write.table with fwrite
#65
bschilder
closed
2 years ago
1
Make dedicated liftover function
#64
bschilder
closed
2 years ago
2
Run `plot_chromHMM` example
#63
bschilder
closed
2 years ago
2
Require `TxDb.Hsapiens.UCSC.**.knownGene`
#62
bschilder
closed
2 years ago
1
Use multiple genome builds
#61
bschilder
closed
2 years ago
10
Explain what the picard summary file is
#60
NathanSkene
closed
2 years ago
0
`error in evaluating the argument 'x' in selecting a method for function 'elementMetadata': GRanges objects don't support [[`
#59
bschilder
closed
2 years ago
8
`import_narrowPeak`
#58
bschilder
closed
2 years ago
1
Fix GHA
#57
bschilder
closed
2 years ago
1
repairs needed for Bioconductor submission
#56
vjcitn
closed
2 years ago
1
add distance away from centre plot
#55
serachoi1230
closed
2 years ago
0
Add venn diagram
#54
serachoi1230
closed
2 years ago
0
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