3
votes
18
replies
3.0k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
10 months ago • updated 4 weeks ago shepherl 3.9k
7
votes
28
replies
6.2k
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
750
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
11 weeks ago • updated 25 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 11.4 years ago by ▴ 280
2
votes
6
replies
2.6k
views
Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error cn.mops
updated 10 weeks ago by • 0 • written 6.3 years ago by ▴ 10
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 6 weeks ago by 50k • written 9.8 years ago by ▴ 40
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
3
votes
5
replies
1.7k
views
Error: 'IdClusters'
DECIPHER
updated 11 months ago by ▴ 10 • written 15 months ago by • 0
0
votes
7
replies
460
views
DESeq2 filtering vs edgeR filtering
DESeq2
9 weeks ago • updated 7 weeks ago fr8712ca-s • 0
4
votes
16
replies
7.4k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 8 weeks ago by • 0 • written 9.0 years ago by ▴ 150
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 9.0 years ago by ▴ 120
0
votes
5
replies
1.2k
views
pathway finding software
written 15.5 years ago by ▴ 250
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
13
votes
22
replies
27k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 12 weeks ago by 42k • written 7.9 years 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 8 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 10.4 years ago by ★ 13k
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 10 months ago by 65k • written 10 months ago by • 0
1
vote
10
replies
2.1k
views
Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 18 months ago by • 0
2
votes
3
replies
1.7k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 8 months ago by 50k • written 8 months ago by • 0
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 3 days ago by ▴ 220 • written 6.7 years ago by ▴ 80
5
votes
8
replies
4.0k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
0
votes
4
replies
758
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
12 months ago sreeshmaraj72 • 0
4
votes
13
replies
1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 42k • written 8 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
0
votes
3
replies
1.8k
views
extract rsids of SNPs using their genomic positions
rsids SNPlocs.Hsapiens.dbSNP150.GRCh38
written 10 months ago by • 0
1
vote
13
replies
11k
views
unable to access index for repository
Bioconductor ConsensusClusterPlus
updated 9 months ago by • 0 • written 17 months ago by • 0
9
votes
11
replies
6.0k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 9 weeks ago by 3.9k • written 2.3 years ago by ▴ 40
7
votes
39
replies
5.8k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 1 day ago by • 0 • written 5.5 years ago by ★ 4.0k
1
vote
4
replies
2.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 18 months ago by • 0
2
votes
7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
2
votes
3
replies
1.1k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 4 months ago by • 0 • written 2.9 years ago by ▴ 470
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 10 months ago by ▴ 180 • written 17 months ago by ▴ 30
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 5 days ago by 42k • written 15 months ago by • 0
2
votes
8
replies
564
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks 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
6
replies
1.5k
views
mailman bugs
Website
21.3 years ago • updated 11 months ago Gordon Smyth 50k
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
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
4
votes
3
replies
1.0k
views
WGCNA documentation not available
WGCNA
written 5 months ago by ▴ 10
0
votes
7
replies
2.7k
views
LIMMA: plotMDS
updated 9 months ago by 50k • written 12.0 years ago by ▴ 180
4
votes
10
replies
1.8k
views
Archives prior to 3.15 gone
archive bioconductor
updated 6 months ago by 3.9k • written 20 months ago by ▴ 30
0
votes
6
replies
1.3k
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 11 weeks ago by 50k • written 19.1 years ago by ★ 1.1k
1
vote
5
replies
1.7k
views
rowsum or similar for RleArray?
delayedarray rowsum
written 6.7 years ago by ▴ 180
0
votes
7
replies
1.7k
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
3
votes
7
replies
5.5k
views
error with champ.load
champ
written 6.5 years ago by ▴ 10
2
votes
3
replies
841
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
0
votes
11
replies
2.1k
views
globaltest question
Pathways probe affy Pathways probe affy
written 17.7 years ago by ▴ 30
1
vote
16
replies
3.4k
views
error in ChAMP loading file
ChAMP
updated 9 weeks ago by • 0 • written 18 months ago by • 0
2
votes
3
replies
713
views
Rsubread: subjunc() loads index repeatedly
Rsubread
10 months ago • updated 9 months ago Gerhard Thallinger ▴ 180
1,737 results • Page 1 of 35
Recent ...
Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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