3
votes
18
replies
2.9k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
10 months ago • updated 17 days ago shepherl 3.9k
7
votes
28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 3 months ago by 50k • written 9.2 years ago by ★ 7.9k
0
votes
7
replies
692
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
9 weeks ago • updated 11 days ago shepherl 3.9k
0
votes
21
replies
6.6k
views
BAM files to Genomic Ranges object
Alignment convert Repitools Alignment convert Repitools
updated 5 months ago by • 0 • written 11.3 years ago by ▴ 280
2
votes
6
replies
2.5k
views
Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error cn.mops
updated 8 weeks ago by • 0 • written 6.3 years ago by ▴ 10
1
vote
8
replies
1.5k
views
News: Final List of Deprecated Package Bioc 3.9
deprecation release software experimentData News
written 5.1 years ago by 3.9k
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 4 weeks ago by 50k • written 9.8 years ago by ▴ 40
0
votes
5
replies
5.8k
views
masigpro Error in terms.formula(formula, data = data) : '.' in formula and no 'data' argument
masigpro
updated 9 months ago by • 0 • written 8.9 years ago by ▴ 120
3
votes
5
replies
1.7k
views
Error: 'IdClusters'
DECIPHER
updated 11 months ago by ▴ 10 • written 14 months ago by • 0
0
votes
5
replies
1.1k
views
pathway finding software
written 15.5 years ago by ▴ 250
2
votes
11
replies
1.6k
views
Not able to download recount3 data
recount3
updated 12 months ago by ★ 1.0k • written 16 months ago by ▴ 20
13
votes
22
replies
27k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 10 weeks ago by 41k • written 7.9 years ago by ▴ 30
1
vote
6
replies
2.7k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.5 years ago by ▴ 10
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 6 weeks ago by • 0 • written 9.0 years ago by ▴ 150
0
votes
7
replies
431
views
DESeq2 filtering vs edgeR filtering
DESeq2
7 weeks ago • updated 5 weeks ago fr8712ca-s • 0
2
votes
9
replies
1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 6 months ago by ▴ 50 • written 6 months ago by ▴ 30
1
vote
3
replies
3.1k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error maftools tcgabiolinks
updated 6 weeks ago by ▴ 20 • written 6.6 years ago by ▴ 100
0
votes
11
replies
3.8k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 3 months ago by ▴ 180 • written 7.1 years ago by ★ 2.0k
0
votes
5
replies
2.0k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation affy oligo ffpe Annotation affy oligo ffpe
written 10.3 years ago by ★ 13k
1
vote
13
replies
11k
views
unable to access index for repository
Bioconductor ConsensusClusterPlus
updated 9 months ago by • 0 • written 16 months ago by • 0
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
7
replies
2.7k
views
LIMMA: plotMDS
updated 9 months ago by 50k • written 12.0 years ago by ▴ 180
1
vote
10
replies
2.0k
views
Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 17 months ago by • 0
0
votes
6
replies
1.2k
views
LIMMA : design (1, 2, 3, 3 ) , I got EXCITING results, what could be the logic, since i have 2 replicates for 3rd group only ?
affy affy
updated 9 weeks ago by 50k • written 19.0 years ago by ★ 1.1k
1
vote
4
replies
2.5k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 17 months ago by • 0
0
votes
4
replies
743
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
1
vote
5
replies
1.7k
views
rowsum or similar for RleArray?
delayedarray rowsum
written 6.7 years ago by ▴ 180
4
votes
3
replies
924
views
WGCNA documentation not available
WGCNA
written 5 months ago by ▴ 10
0
votes
3
replies
1.7k
views
extract rsids of SNPs using their genomic positions
rsids SNPlocs.Hsapiens.dbSNP150.GRCh38
written 9 months ago by • 0
3
votes
7
replies
5.4k
views
error with champ.load
champ
written 6.5 years ago by ▴ 10
0
votes
3
replies
2.5k
views
Background correction with neqc
Normalization Cancer Normalization Cancer
updated 6 months ago by 50k • written 12.4 years ago by ★ 13k
0
votes
7
replies
1.6k
views
Unable to install RefPlus - R=4.3.1, BiocManager=3.18
Install instal
updated 6 months ago by 65k • written 6 months ago by • 0
1
vote
16
replies
3.3k
views
error in ChAMP loading file
ChAMP
updated 7 weeks ago by • 0 • written 17 months ago by • 0
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by • 0
2
votes
3
replies
685
views
Rsubread: subjunc() loads index repeatedly
Rsubread
9 months ago • updated 8 months ago Gerhard Thallinger ▴ 180
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
2
votes
3
replies
1.1k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 3 months ago by • 0 • written 2.8 years ago by ▴ 470
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 9 months ago by • 0 • written 8.4 years ago by ▴ 60
0
votes
6
replies
1.5k
views
mailman bugs
Website
21.2 years ago • updated 10 months ago Gordon Smyth 50k
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
2
votes
3
replies
810
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 9 months ago by ▴ 180 • written 17 months ago by ▴ 30
7
votes
18
replies
3.0k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 4 months ago by ▴ 240 • written 7.1 years ago by ▴ 20
4
votes
13
replies
1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
2
votes
3
replies
1.6k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
4
votes
10
replies
1.8k
views
Archives prior to 3.15 gone
archive bioconductor
updated 6 months ago by 3.9k • written 19 months ago by ▴ 30
2
votes
6
replies
1.3k
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 12 months ago by ★ 1.0k • written 17 months ago by • 0
6
votes
5
replies
1.2k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 8 months ago by ▴ 740 • written 9 months ago by ▴ 20
0
votes
11
replies
2.0k
views
globaltest question
Pathways probe affy Pathways probe affy
written 17.7 years ago by ▴ 30
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 4 weeks ago by • 0 • written 5.5 years ago by ★ 3.9k
1,744 results • Page 1 of 35
Recent ...
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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. …
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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…
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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 …
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It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
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This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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