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
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
7
votes
18
replies
2.9k
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
0
votes
17
replies
3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 10 months ago by • 0 • written 6.6 years ago by • 0
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.2 years ago by ▴ 10
2
votes
2
replies
389
views
"Details" section for specific software packages
Website
updated 6 months ago by ★ 6.5k • written 6 months ago by • 0
1
vote
3
replies
1.8k
views
Making MDS plot
plotMDS limma
updated 10 months ago by 50k • written 10 months ago by • 0
2
votes
3
replies
2.2k
views
Keep getting this error "Warning: unable to access index for repository"?
CATALYST
updated 11 months ago by 16k • written 11 months ago by ▴ 20
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.2 years ago by • 0
1
vote
3
replies
892
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
updated 10 months ago by • 0 • written 11 months ago by • 0
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 18 months ago by ▴ 20
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 29 days ago by • 0 • written 5.2 years ago by • 0
1
vote
3
replies
461
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 4 months ago by • 0 • written 4 months ago by • 0
2
votes
3
replies
2.2k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 6 weeks ago by ★ 4.1k • written 2.1 years ago by ▴ 20
3
votes
4
replies
8.6k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.8 years ago by ▴ 30
0
votes
2
replies
553
views
Heat Map
ColData pheatmap DESeq2
written 10 months ago by • 0
4
votes
4
replies
3.4k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 3.2 years ago by ▴ 20
0
votes
2
replies
821
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 8 months ago by 41k • written 8 months ago by • 0
0
votes
3
replies
1.5k
views
Recount3 error with default "recount3_url" option
recount3
updated 12 months ago by ★ 1.0k • written 17 months ago by ▴ 110
0
votes
3
replies
145
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 13 days ago by 65k • written 13 days ago by ▴ 30
2
votes
2
replies
180
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 13 days ago by 65k • written 14 days ago by • 0
3
votes
8
replies
902
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils droplet
written 5 months ago by ▴ 10
0
votes
3
replies
1.2k
views
News: European Bioconductor Conference 2023 planning
Europe Conference EuroBioC Events News
updated 11 days ago by • 0 • written 18 months ago by ▴ 70
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by • 0
4
votes
9
replies
1.3k
views
DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 8 months ago by ▴ 10 • written 8 months ago by ▴ 10
4
votes
7
replies
859
views
weird volcano plot
DESeq2
updated 8 weeks ago by • 0 • written 5 months ago by ▴ 10
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 5 months ago by ▴ 730 • written 3.0 years ago by • 0
8
votes
9
replies
1.1k
views
All three of the sites where genomeinfodbdata R packages are stored appear to be down.
GenomeInfoDbData
8 months ago 15753563659 ▴ 50
2
votes
2
replies
1.5k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 3.4 years ago by ★ 1.5k
9
votes
38
replies
6.8k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.2 years ago by ▴ 190
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 5 months ago by • 0 • written 6.5 years ago by ▴ 60
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
12 months ago • updated 11 months ago Luis • 0
2
votes
5
replies
1.3k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 8 months ago by 50k • written 8 months ago by • 0
3
votes
6
replies
960
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge OrganismData OrganismDb
10 months ago abhisek001 • 0
3
votes
3
replies
360
views
plotUMAP Gene Set Faceted
scater
updated 3 months ago by ▴ 160 • written 3 months ago by ★ 1.5k
0
votes
2
replies
874
views
News: List of Deprecated Packages for Bioc3.17
Bioconductor Deprecation Devel devel
12 months ago • updated 11 months ago shepherl 3.9k
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by • 0 • written 9.2 years ago by ▴ 40
1
vote
4
replies
215
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 10 days ago by 65k • written 14 days ago by • 0
0
votes
2
replies
1.4k
views
about baseMean in DEseq2
DESeq2
written 2.7 years ago by ▴ 670
0
votes
2
replies
269
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
8
votes
12
replies
2.6k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by 41k • written 12 months ago by ▴ 90
0
votes
2
replies
173
views
bioconductor emailing list
Bioconductor
updated 5 weeks ago by 3.9k • written 5 weeks ago by • 0
0
votes
2
replies
802
views
Recount3 data download problem
recount recount3
updated 12 months ago by ★ 1.0k • written 16 months ago by • 0
0
votes
2
replies
616
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
0
votes
4
replies
1.9k
views
how to save subsetted GDS file
gwastools
written 6.0 years ago by ▴ 30
7
votes
6
replies
4.1k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 6 months ago by 690 • written 20 months ago by ▴ 20
0
votes
2
replies
1.2k
views
Error: BiocParallel errors
xcms msdata BiocParallel
8 months ago • updated 7 months ago mavamay • 0
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
10 months ago Ndimensional ▴ 20
0
votes
5
replies
702
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout DESeq2
written 10 months ago by • 0
0
votes
2
replies
474
views
EdgeR FTest
edgeR
updated 8 months ago by 50k • written 8 months ago by • 0
1,000 results • Page 2 of 20
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
Awards • All
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Popular Question to shepherl 3.9k
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Locations • All
France, 4 minutes ago
United Kingdom, 17 minutes ago
WEHI, Melbourne, Australia, 23 minutes ago
Finland, 34 minutes ago
Melbourne, Australia, 42 minutes ago
Traffic: 544 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6