1
vote
7
replies
3.0k
views
U-shape of p-value histograms is removed by filtering for genes that have >5 counts in >10% of samples before applying DESeq2 analysis
deseq2 p-value distribution U-shaped pre-filter low counts
7.0 years ago stu111538 • 0
0
votes
4
replies
3.5k
views
biomaRt: Unexpected format to the list of available marts.
software error biomaRt
7.0 years ago frank007 • 0
0
votes
1
reply
1.3k
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
4
votes
4
replies
1.9k
views
Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
limma stageR decideTests
updated 7.0 years ago by ▴ 180 • written 7.0 years ago by ▴ 180
2
votes
5
replies
2.2k
views
Error loading Gviz package object path is not exported by namespace:Rsamtools
gviz rsamtools
updated 7.0 years ago by • 0 • written 7.0 years ago by • 0
3
votes
7
replies
1.9k
views
Using varianceStabilizingTransformation (VST) with no replications?
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
3
votes
9
replies
3.4k
views
Differential transcript expression (DTE) analysis
rnaseqDTU dtu
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 50
0
votes
0
replies
974
views
TPP error message " The names of the data objects in 'data' differ from the names given in the Experiment column of 'configTable'."
software error TPP
updated 7.0 years ago by 4.3k • written 7.0 years ago by • 0
0
votes
3
replies
2.1k
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 670
0
votes
4
replies
1.7k
views
MSnset combine error message
MSnbase
7.0 years ago kamal.fartiyal84 ▴ 10
2
votes
2
replies
1.6k
views
rnaseqDTU DTU workflow - pots-hoc Filter
DTU DRIMSeq rnaseqDTU
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 60
0
votes
5
replies
5.0k
views
Errors installing RforProteomics and MSnbase packages
RforProteomics MSnbase
updated 7.0 years ago by 1.6k • written 7.0 years ago by ▴ 10
1
vote
2
replies
1.8k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 7.0 years ago by ▴ 980 • written 7.0 years ago by ▴ 270
0
votes
3
replies
2.1k
views
extracting scaffoldnames from HiC contact matrix
hic
updated 7.0 years ago by • 0 • written 7.0 years ago by • 0
3
votes
7
replies
1.8k
views
Limma analysis, controlling for Donors.
limma r microarray
updated 7.0 years ago by 53k • written 7.0 years ago by • 0
1
vote
0
replies
1.0k
views
Job: NGS Technical Applications Scientist
#sequencing #NGS #FAS #fieldsupport Job
7.0 years ago paul ▴ 10
1
vote
1
reply
1.7k
views
DESeq2 - lfcShrink with list contrast on grouped variable
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
3
votes
3
replies
1.8k
views
limma for getting DEGs from my own input matrix
limma
updated 7.0 years ago by ★ 29k • written 7.0 years ago by • 0
2
votes
1
reply
1.1k
views
Go back to GRanges used as RaggedExperiment input
RaggedExperiment
updated 7.0 years ago by 700 • written 7.0 years ago by ▴ 40
2
votes
2
replies
1.7k
views
What can be done to separate the healthy and patient samples in PCA plot and Distance matrix
deseq2 PCAplot Visualization
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
votes
7
replies
1.8k
views
DeSeq2 Ribosome Profiling: multiple factor design
deseq2 design timeseries
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 20
4
votes
3
replies
1.7k
views
RSubread in cygwin
subread
7.0 years ago Diana ▴ 10
1
vote
1
reply
1.8k
views
read.FCS memory limit? - $PnRNAis larger than R's numeric limit
flowCore read.FCS memory_limit
7.0 years ago lloyd.izard ▴ 80
0
votes
1
reply
1.6k
views
consulting about the FELLA package
software error FELLA
updated 7.0 years ago by ▴ 20 • written 7.0 years ago by • 0
1
vote
6
replies
2.3k
views
edgeR for time series
edgeR
updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 40
0
votes
3
replies
2.2k
views
How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 7.0 years ago by ▴ 10 • written 7.0 years ago by • 0
0
votes
0
replies
856
views
WEBBIOC
updated 7.0 years ago by 0 • written 19.4 years ago by ▴ 10
2
votes
10
replies
4.4k
views
ChIPpeakAnno, MACS format annotation
bioconductor ChIPpeakAnno
updated 7.0 years ago by ★ 4.3k • written 8.8 years ago by ▴ 30
3
votes
6
replies
1.6k
views
Handling multiple knockout experiments with DESeq2
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
votes
0
replies
1.4k
views
ath1121501probe_1.0 error (was GCRMA missing value error on ATH1 chip)
probe affy probe affy
updated 7.0 years ago by 0 • written 21.9 years ago by ▴ 940
0
votes
1
reply
893
views
signeR errors when assessing for variant signatures
software error
updated 7.0 years ago by ▴ 10 • written 7.0 years ago by • 0
0
votes
0
replies
800
views
R ArrayExpress probleme
R
7.0 years ago hafidimustapha • 0
2
votes
4
replies
3.8k
views
Problem installing GenomicRanges package
software error
7.0 years ago aigofaith ▴ 10
0
votes
1
reply
1.7k
views
Help on contrast matrix Limma
updated 7.0 years ago by 0 • written 16.3 years ago by 53k
0
votes
0
replies
994
views
kegg enrichment using clusterProfiler could not provide gene name
annotation
7.0 years ago huangzhiguang2016 • 0
0
votes
1
reply
2.1k
views
gcrma background correction-saving output
cdf affy gcrma matchprobes affyio cdf affy gcrma matchprobes affyio
updated 7.0 years ago by 0 • written 19.1 years ago by ★ 2.2k
0
votes
2
replies
1.4k
views
VCF files incompatible with signeR
software error signeR
7.0 years ago Dan • 0
0
votes
1
reply
878
views
error while runing Bioconductro install script
updated 7.0 years ago by 0 • written 22.7 years ago by ▴ 10
1
vote
4
replies
2.5k
views
Error : Salmon tximport to DESeq2
deseq2 tximport
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
votes
0
replies
975
views
error in reading CEL file
updated 7.0 years ago by 0 • written 21.4 years ago by ▴ 80
0
votes
2
replies
1.4k
views
LIMMA: how to assign file name
limma ASSIGN limma ASSIGN
updated 7.0 years ago by 0 • written 20.7 years ago by ▴ 180
0
votes
1
reply
1.8k
views
flowDensity loop on flowSet
flowdensity flowcore for loop
updated 7.0 years ago by 0 • written 7.2 years ago by • 0
0
votes
1
reply
1.3k
views
Add interaction term between variables to DEXSeq design
DEXSeq interaction
7.0 years ago zhenzuo2 • 0
0
votes
0
replies
1.4k
views
Job: Postdoc in Bioinformatics (UCSF Benioff Children's Hospital Oakland)
Bioinformatics RNA-seq Postdoc Genomics Statistical model Job
7.0 years ago djawaheer • 0
0
votes
5
replies
2.6k
views
Error:no method for coercing this S4 class to a vector
annotation genomation
updated 7.0 years ago by ▴ 20 • written 7.0 years ago by • 0
0
votes
3
replies
2.1k
views
tri.counts.method parameter in deconstructSigs
deconstructsigs
updated 7.0 years ago by 0 • written 9.0 years ago by ▴ 90
1
vote
0
replies
1.3k
views
Job: Staff researcher position in biostatistics / data science consulting at EMBL
EMBL Job
7.0 years ago Wolfgang Huber ★ 13k
0
votes
0
replies
1.3k
views
error importing bam file for MEDIPS analysis
MEDIPS bamfile
updated 7.0 years ago by 0 • written 7.2 years ago by • 0
0
votes
3
replies
2.4k
views
Algorithm for between and within microarray normalisation (for meta-analysis).
microarray meta-analysis gene expression
updated 7.0 years ago by 0 • written 9.5 years ago by ▴ 70
6
votes
14
replies
3.8k
views
Paired analysis setup using edgeR - follow up question
edger
7.0 years ago candida.vaz ▴ 50
46,715 results • Page 231 of 935
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Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner • 0
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
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Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
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The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
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Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
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Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
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