Showing : bug • reset
21
votes
24
replies
13k
views
Problem with biomart's listMarts function
biomart bug
updated 8.0 years ago by ▴ 470 • written 8.5 years ago by ★ 2.0k
9
votes
2
replies
8.8k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 2.7 years ago by 41k • written 7.2 years ago by ▴ 10
6
votes
3
replies
2.1k
views
Possible bug in Rsubread Phred-Score read
rsubread bug alignment
updated 9.5 years ago by ★ 3.6k • written 9.5 years ago by ▴ 20
5
votes
16
replies
2.3k
views
GSVA package scores are opposite on mac and windows
GSVA bug gsva bugs
updated 6.6 years ago by ★ 3.3k • written 6.6 years ago by ▴ 10
4
votes
2
replies
831
views
TENxPBMCData error loading PBMC4k data
bug TENxPBMCData
3.5 years ago zhe ▴ 20
3
votes
2
replies
1.4k
views
Crash GSVA 1.24.0 with bootstrapping
GSVA bug
updated 7.0 years ago by ★ 3.3k • written 7.0 years ago by ▴ 20
3
votes
2
replies
1.4k
views
Bug: estimateSizeFactors in DESeq2 doesn't work with a single normalization control
deseq2 bug
updated 9.2 years ago by 41k • written 9.2 years ago by ★ 2.0k
3
votes
4
replies
1.2k
views
Does Rsamtools support tag names with number characters? i.e ."B1"
rsamtools bug
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
3
votes
6
replies
1.1k
views
How to replace NAs values in "CompressedIntegerList" objects [reproducible example is included] ?
r bug granges
8.1 years ago Jurat Shahidin ▴ 80
3
votes
2
replies
1.9k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 6.2 years ago by 16k • written 6.2 years ago by ▴ 10
3
votes
4
replies
1.6k
views
Different geneset same p-values in topGO
topgo bug
7.3 years ago • updated 3.6 years ago Lluís Revilla Sancho ▴ 730
3
votes
5
replies
1.7k
views
Selecting few ids from reactome.db
annotationdbi reactome.db bug
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 730
3
votes
3
replies
2.6k
views
Transcripts in TxDb.Hsapiens.UCSC.hg38.knownGene but not in ucsc genome brower
annotation txdb.hsapiens.ucsc.hg38.knowngene bug
7.6 years ago shilin.zhao ▴ 40
3
votes
2
replies
1.6k
views
EBImage read png causes R to crash
ebimage bug
8.5 years ago Henning Redestig ▴ 20
3
votes
2
replies
2.5k
views
Rqc - envir must be either NULL, a list, or an environment.
software error bug library
updated 7.3 years ago by ▴ 70 • written 7.3 years ago by ▴ 10
2
votes
3
replies
1.2k
views
Probable bug in GSEABase package.
software error bug gseabase
7.3 years ago jcrodriguez ▴ 20
2
votes
1
reply
1.9k
views
Cummerbund error column name mismatch
cummerbund bug error
6.8 years ago tannerndrsn4 ▴ 20
2
votes
1
reply
1.5k
views
Possible bug: outdated result from listDatabases()
KEGGREST bug
updated 6.7 years ago by ▴ 50 • written 6.7 years ago by • 0
2
votes
1
reply
1.2k
views
Bug Report for R Package "EBImage": log(image, base=2) is same as log(*) (natural log) instead of log2 (base 2).
bug ebimage
updated 8.5 years ago by ▴ 750 • written 8.5 years ago by ▴ 20
2
votes
4
replies
2.1k
views
topGO crashes with ' argument "annotationFun" is missing, with no default'
bug topGO
updated 7.4 years ago by 65k • written 7.4 years ago by ▴ 160
1
vote
1
reply
1.2k
views
Error in intI when plotting igraph graph.
bug netbiov
8.2 years ago sakan1000 ▴ 10
1
vote
3
replies
1.2k
views
Unable to set colors in plotrt function in xcms package
xcms bug
9.0 years ago Johannes Rainer ★ 2.0k
1
vote
13
replies
3.0k
views
Several issues with the package easyRNASeq
easyrnaseq bug
8.8 years ago Michael Dondrup ▴ 10
1
vote
5
replies
1.9k
views
biomaRt crashes when result contains missing values
biomaRt bug
updated 7.9 years ago by ★ 6.5k • written 7.9 years ago by • 0
1
vote
0
replies
922
views
Length of a region incorrectly calculated
coverageview bug
8.3 years ago balwierz ▴ 40
1
vote
1
reply
1.1k
views
Downloading Thymoma data (THYM)
TCGAbiolinks bug
8.1 years ago Marcel Ramos 690
1
vote
2
replies
1.2k
views
Downloading bt.exon_quantification with TCGAbiolinks
tcgabiolinks bug
8.1 years ago Marcel Ramos 690
1
vote
2
replies
1.5k
views
TCGAbiolinks 403 Forbidden Error
bug issue tcgabiolinks
updated 7.8 years ago by ▴ 270 • written 7.9 years ago by 690
1
vote
6
replies
4.1k
views
Gviz issue: crashing when AnnotationTrack( ... , just.group="above")
software error bug crash Gviz
updated 7.7 years ago by ★ 1.6k • written 7.9 years ago by ▴ 160
1
vote
1
reply
1.7k
views
GSEABase getGmt() fails when more than 1 line contains duplicates
gseabase bug
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 10
1
vote
2
replies
1.9k
views
Error when using multiple heatmaps in ComplexHeatmaps
ComplexHeatmap bug
7.3 years ago brt381 • 0
1
vote
2
replies
1.4k
views
Error in Biostrings with Fastafiles using the carriage return <cr>
biostrings software error bug
updated 7.3 years ago by 16k • written 7.3 years ago by • 0
1
vote
2
replies
1.2k
views
BiocCheck path escape issue
bioccheck bug
7.0 years ago Michael Steinbaugh ▴ 90
1
vote
1
reply
1.1k
views
Bug in Biostrings DNAStringSet(), segfault
bug biostrings
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 10
1
vote
3
replies
1.0k
views
SeqPattern plotPatternOccurrenceAverage problem
SeqPattern bug
5.9 years ago elisheva.h02 • 0
1
vote
1
reply
1.0k
views
rTandem compilation failed
rtandem bug compilation error
5.9 years ago Ed Siefker ▴ 230
1
vote
5
replies
591
views
Manual creation of qPCRset does not work
bug nondetects HTqPCR
updated 6 months ago by • 0 • written 7 months ago by ▴ 230
0
votes
0
replies
883
views
[DSS] callDMR - dis.merge option does not seem to be working
DSS bug troubleshooting callDMR
4.4 years ago matthew.kearney • 0
0
votes
1
reply
865
views
[bug report] som documentation contains incorrect formula
som bug
8.1 years ago balwierz ▴ 40
0
votes
2
replies
1.4k
views
Problem with VariantAnnotation and VCF "R" genotype fields when expanding CollapsedVCF
VariantAnnotation bug
updated 7.4 years ago by ★ 6.8k • written 7.4 years ago by 21k
0
votes
2
replies
1.7k
views
Problem with GeneSetCollection after updating R devel packages.
bug gseabase example
7.2 years ago jcrodriguez ▴ 20
0
votes
1
reply
1.2k
views
BiocParallel-1.4.0 bplapply bug when using nested lists and MulticoreParam
biocparallel bug
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by • 0
0
votes
3
replies
1.3k
views
rtracklayer v1.30.0 can no longer import gff files
rtracklayer import.gff3 bug
updated 8.5 years ago by 16k • written 8.5 years ago by ★ 2.0k
0
votes
0
replies
1.0k
views
beadarray: Make grep in readSamplesheet case insensitive
beadarray bug
7.0 years ago S. K. • 0
0
votes
1
reply
1.2k
views
pheatmap needs to be manually added to plot heatmaps
singler bug
4.1 years ago muad.abdelhay ▴ 10
0
votes
3
replies
1.4k
views
possible conflict between renameSeqLevels (TxDb) and isActiveSeq (TxDb)
bug txdb genomicfeatures
8.7 years ago • updated 8.6 years ago Robert K. Bradley ▴ 40
0
votes
0
replies
1.3k
views
OmicCircos: included UCSC.hg19.chr dataframe is actually hg18 cytobands
omiccircos bug hg19 hg18 data
7.0 years ago matthew.bashton • 0
0
votes
0
replies
947
views
sangerseqR::read.abif reads float data incorrectly on little-endian systems
sangerseqR bug
7.0 years ago brendan.furneaux ▴ 10
0
votes
9
replies
3.4k
views
rhdf5 32-bit unsigned int issue
rhdf5 bug
updated 8.8 years ago by ▴ 550 • written 8.9 years ago by • 0
0
votes
1
reply
886
views
Identical() fails in Biostrings package
biostrings bug
updated 8.9 years ago by 16k • written 8.9 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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