0
votes
1
reply
1.9k
views
Methread error Error in data[, 5] * data[, 6] : non-numeric argument to binary operator
methylkit
updated 4.3 years ago by ▴ 10 • written 4.6 years ago by • 0
2
votes
1
reply
2.7k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
1
reply
2.6k
views
Gene level methylation values
methylation methylKit bsseq
updated 4.3 years ago by ▴ 10 • written 4.5 years ago by ▴ 80
0
votes
3
replies
1.8k
views
small log2foldChange value in the most significant genes
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
1
reply
1.0k
views
Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 20
0
votes
1
reply
1.5k
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data RNASeqR Normalization BatchEffect
updated 4.3 years ago by 68k • written 4.3 years ago by ▴ 20
2
votes
3
replies
2.6k
views
biomart query in R is not matching ensembl website - missing results
ensembldb biomaRt
updated 4.3 years ago by ★ 6.6k • written 4.3 years ago by • 0
0
votes
0
replies
1.2k
views
Job: PhD student position: Vertebrate brain origins and evolution
PhD single-cell ComparativeGenomics evolution
4.3 years ago henrik.kaessmann • 0
0
votes
0
replies
1.2k
views
#SeqSQC error: Problem while converting vcf format to gds format
SNPRelate gdsfmt SeqSQC
4.3 years ago Bhargavi • 0
2
votes
3
replies
1.4k
views
edgeR contrasts confusion when multiple groups are involved
edgeR
updated 4.3 years ago by 53k • written 4.3 years ago by • 0
4
votes
3
replies
1.8k
views
Problem opening hdf5 files previously created with HDF5Array functions
HDF5Array
updated 4.3 years ago by ★ 6.6k • written 4.3 years ago by ▴ 20
2
votes
2
replies
1.4k
views
Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
4.3 years ago • updated 2.7 years ago diangomaiga • 0
0
votes
3
replies
1.2k
views
What's the difference between formatC() and round() function when used to limite digits numbers?
round formatC
4.3 years ago Yang • 0
0
votes
0
replies
1.2k
views
Job: Bioinformatics postdoc in comparative genomics
single-cell evolution Genomics Postdoc
4.3 years ago henrik.kaessmann • 0
0
votes
1
reply
1.3k
views
Get CHR & POS for a list of SNP rs ids (>1M)
POS CHR SNP rs
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
4
votes
4
replies
2.6k
views
biomaRt error: database disk image is malformed
biomaRt
updated 2.7 years ago by • 0 • written 4.3 years ago by ▴ 10
0
votes
2
replies
981
views
where the gene is overexpressed and down regulated while doing DESeq2 analysis
DESe DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
3
votes
4
replies
3.4k
views
How to get the list of genes from DiffBind dba.report or dba.peakset
diffbind
updated 4.3 years ago by ▴ 10 • written 7.5 years ago by ▴ 10
0
votes
1
reply
2.1k
views
[CSAW] Erreur : Negative counts not allowed
csaw
4.3 years ago Nicolas Servant ▴ 260
0
votes
0
replies
416
views
read.LC480 format 384 wells
LC480
4.3 years ago Sebastian • 0
3
votes
1
reply
1.2k
views
News: Service problems noted
bioconductor
updated 4.3 years ago by 4.3k • written 4.3 years ago by 6.7k
2
votes
4
replies
5.0k
views
BiocManager::install() does not work anymore
Install PackageType
updated 4.3 years ago by 4.3k • written 4.3 years ago by • 0
0
votes
2
replies
2.1k
views
Unable to open igraph.so even though the file is present.
enrichplot clusterProfiler R
4.3 years ago Adarsh • 0
0
votes
1
reply
994
views
stageR p-adj values of zero
stageR
updated 4.3 years ago by ▴ 180 • written 4.3 years ago by • 0
0
votes
2
replies
1.4k
views
FlowSOM dependencies - cytoML and flowutils
FlowSOM
4.3 years ago jakub.savara • 0
0
votes
1
reply
3.6k
views
how to sort y-axis category of GO result
GO.db clusterProfiler dotplot barplot
4.3 years ago Yang • 0
7
votes
12
replies
6.4k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR normalization fastq txt TMM
updated 3.7 years ago by 53k • written 10.2 years ago by • 0
0
votes
2
replies
1.4k
views
How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR DifferentialExpression TMM RNASeq
updated 4.3 years ago by 53k • written 4.3 years ago by • 0
3
votes
3
replies
1.6k
views
Is it advisable to input a count matrix that consists of reads aligned using different algorithms (HT-Seq and Salmon)?
DESeq2
updated 4.3 years ago by ★ 1.4k • written 4.3 years ago by • 0
4
votes
13
replies
3.5k
views
Speeding up of DelayedArray::write_block()
HDF5Array DelayedArray
updated 2.3 years ago by 16k • written 4.3 years ago by ▴ 10
2
votes
2
replies
1.2k
views
Vignette output - BiocSytle::html_document
BiocStyle
4.3 years ago ullrich ▴ 20
0
votes
2
replies
3.0k
views
Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
4.3 years ago p.l.chen • 0
2
votes
5
replies
7.1k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 3.4 years ago by ▴ 20 • written 4.3 years ago by ▴ 20
1
vote
2
replies
1.1k
views
Extracting the LFC from a reduced model
DESeq2
4.3 years ago Sonia • 0
0
votes
0
replies
898
views
Need help in plotting RNA-seq foldchange values in circos plot
Circos
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
3
replies
1.9k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 3.4 years ago by ★ 5.2k • written 4.3 years ago by ▴ 40
2
votes
4
replies
4.5k
views
enrichDGN result can't be visualised by barplot
enrichplot
4.3 years ago Pahi ▴ 10
2
votes
2
replies
9.9k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by ▴ 10
0
votes
0
replies
858
views
How to find genomic position
circRNAprofiler R
4.3 years ago suxxa ▴ 20
1
vote
2
replies
1.4k
views
How to apply a function to a RleViesList object?
Views IRanges GRanges RleList
updated 4.3 years ago by ★ 6.6k • written 4.3 years ago by ★ 1.5k
0
votes
0
replies
1.4k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
4.3 years ago Drew • 0
1
vote
2
replies
1.8k
views
DiffBind in Bioconda
DiffBind Bioconda Versions
4.3 years ago Riba Michela ▴ 90
1
vote
0
replies
2.2k
views
documentation on clusterProfiler output
clusterProfiler KEGG
4.3 years ago rafaela.perez ▴ 10
1
vote
2
replies
1.2k
views
Unequal sample pools
limma pooling
4.3 years ago Jenny G • 0
0
votes
0
replies
1.0k
views
Over-enrichment of cytobands in INDUCE-Seq
enrichment INDUCE-Seq
4.3 years ago Mark Dunning ★ 1.1k
0
votes
1
reply
1.4k
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 4.3 years ago by ▴ 780 • written 4.3 years ago by • 0
1
vote
2
replies
2.5k
views
DESeq2 differential expression analysis of protein coding genes only
DESeq2
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by • 0
1
vote
1
reply
2.2k
views
GVIZ on R not loading mm10 from UCSC
Gviz
4.3 years ago RUser743 • 0
0
votes
0
replies
1.2k
views
Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
4.3 years ago lpinello • 0
0
votes
3
replies
1.5k
views
DESeq2 design formula
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
46,730 results • Page 111 of 935
Recent ...
Replies
Comment: chemmineOB install help by Jeremy • 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Awards • All
Popular Question to ATpoint ★ 5.0k
Popular Question to Martin Morgan 25k
Teacher to Michael Love 43k
Popular Question to A • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Locations • All
Switzerland, 12 minutes ago
The city by the bay, 21 minutes ago
Vietnam, 2 hours ago
Singapore, 2 hours ago
United States, 3 hours ago
Traffic: 735 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