3
votes
2
replies
2.3k
views
Issue with pandoc-citeproc when rendering the f1000 article Rmd file from BiocWorkFlowTools
BiocWorkflowTools rmarkdown
updated 8.6 years ago by ▴ 750 • written 8.6 years ago by ★ 1.1k
4
votes
5
replies
2.0k
views
Warning: missing reverse strand option in easyRNASeq.
easyrnaseq rnaseq strand
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 10
1
vote
3
replies
1.8k
views
Deseq2 tissue specific genes
deseq2
8.6 years ago madhusudhana.janga • 0
0
votes
1
reply
1.6k
views
DEXseq reads all in ambiguous_readpair_position and empty categories
dexseq reads
8.6 years ago 514028929 • 0
0
votes
6
replies
2.1k
views
DESeq2: group-group distance analysis (not only sample-sample distance)?
deseq2
8.6 years ago KimS • 0
0
votes
1
reply
2.7k
views
Error computing metrics with ChIPQC (Bioconductor v3.5, ChIPQC v2.1.12)
chipqc chipqcreport
updated 8.6 years ago by ▴ 420 • written 8.6 years ago by • 0
1
vote
4
replies
2.3k
views
TarSeqQC TargetExperiment() Error- failed to stop SOCKcluster cluster-error writing to connection
TarSeqQC R ngs biocparallel
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 10
0
votes
2
replies
1.5k
views
TarSeqQC TargetExperiment() example takes forever
TarSeqQC
updated 8.6 years ago by ▴ 10 • written 9.1 years ago by • 0
0
votes
1
reply
4.1k
views
Import .mtx file in R
sc3
updated 8.6 years ago by ▴ 150 • written 8.6 years ago by • 0
0
votes
1
reply
2.1k
views
Save multiple plots into single pdf from Deseq2 analysis?
plot pdf dev.off
updated 8.6 years ago by ★ 13k • written 8.6 years ago by • 0
5
votes
3
replies
2.3k
views
Is it possible to get Ensembl gene descriptions with ensembldb?
ensembldb
updated 8.6 years ago by ★ 2.1k • written 8.6 years ago by ▴ 90
1
vote
3
replies
2.3k
views
limma regularization on Ballgown
ballgown limma
updated 8.6 years ago by ▴ 210 • written 8.6 years ago by ▴ 10
0
votes
6
replies
2.2k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
8.6 years ago lanhuong ▴ 20
1
vote
3
replies
949
views
Design and Different contrast results with betaPrior
deseq2
8.6 years ago bkrajacich • 0
0
votes
1
reply
976
views
Binding site overlaps
diffbind
updated 8.6 years ago by ★ 5.2k • written 8.6 years ago by • 0
0
votes
1
reply
2.6k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2 tpm heatmap pheatmap
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 40
0
votes
0
replies
1.1k
views
Testing a gene set with globaltest
globaltest
8.6 years ago Lluís Revilla Sancho ▴ 760
5
votes
17
replies
2.9k
views
DiffBind : More fragment sizes than libraries
diffbind
updated 8.6 years ago by ★ 5.2k • written 8.6 years ago by ▴ 60
0
votes
14
replies
3.8k
views
got 0 significant differential bound (DB)
diffbind
8.6 years ago mforoo1 • 0
4
votes
3
replies
3.2k
views
Why does Deseq, Deseq2, and EdgeR give vastly different results.
edger deseq deseq2
8.6 years ago michael.steffen ▴ 20
0
votes
1
reply
1.2k
views
DEsubs problems with Mus musculus
DEsubs
8.6 years ago Rtist • 0
1
vote
3
replies
3.1k
views
DESeq2 estimateDispersionsGeneEst error
deseq2
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
0
votes
0
replies
1.2k
views
Analyzing "Hitachi human oligo chip-drug responsive genes" platform data
microarray analysis
8.6 years ago arisarkar88 ▴ 40
0
votes
1
reply
1.1k
views
How to extract DEG using limma at threshold value p<0.05 and fold change >1.5 ?
limma microarray R bioconductor
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
0
votes
3
replies
2.6k
views
Problem with upgrading Bioconductor from 3.4 to 3.5
Upgrade problem
8.6 years ago michal.combik • 0
1
vote
1
reply
1.1k
views
esearch in reutils package: how to specify dataset?
R
8.6 years ago ezrabekele17 • 0
1
vote
3
replies
1.6k
views
ChIPQC installation does not force latest DiffBind version
chipqc diffbind chipqcreport
updated 8.6 years ago by ▴ 420 • written 8.6 years ago by ▴ 50
3
votes
1
reply
6.0k
views
Creating a count matrix from 8 bam files in R (RNAseq experiment)
deseq2 rnaseq count matrix galignments granges
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
1
vote
2
replies
1.5k
views
ChIPQC report missing figures
chipqc software error
updated 8.6 years ago by ▴ 420 • written 8.6 years ago by ▴ 30
2
votes
1
reply
2.1k
views
ChIPQC with GRCh38/hg38 requires manual loading of hg38 annotation
chipqc
updated 8.6 years ago by ▴ 420 • written 8.6 years ago by ▴ 50
2
votes
5
replies
6.4k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2 results contrast padj
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
0
votes
4
replies
2.8k
views
Problem in extracting a row from matrix in rhdf5
rhdf5
updated 8.6 years ago by ★ 6.6k • written 8.7 years ago by • 0
0
votes
3
replies
3.3k
views
error installing cummeRbund in R studio (Windows desktop)
Rstudio cummerbund error
8.6 years ago mszskb • 0
0
votes
1
reply
1.2k
views
can't install GEOquery
microarray
updated 8.6 years ago by 25k • written 8.6 years ago by • 0
1
vote
1
reply
1.0k
views
The data is not in the file that it should be
pRolocGUI
updated 8.6 years ago by 1.6k • written 8.6 years ago by ▴ 30
0
votes
0
replies
1.1k
views
TCGAbiolinks : TCGAdownload Error in curl
R tcgabiolinks tcgadownload error
8.6 years ago juniuskcc • 0
0
votes
3
replies
2.9k
views
Difference between DESeq2 package version 1.16.1 and 1.14.1
deseq2 pasilla
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
0
votes
0
replies
1.1k
views
Visualize FlowSet by Date
FlowSet data visualization cellcounts
8.6 years ago Maria • 0
0
votes
0
replies
1.1k
views
TSCANorder return less cell number than the raw cell number
TSCAN software error
8.6 years ago yancychy • 0
1
vote
1
reply
1.8k
views
Add flowclust gate to gatingset
opencyto flowclust
updated 8.6 years ago by ★ 1.3k • written 8.6 years ago by ▴ 20
0
votes
1
reply
1.8k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
8.6 years ago bhgyu ▴ 30
0
votes
1
reply
1.3k
views
IDMapper issue in PSICQUIC
PSICQUIC
updated 8.6 years ago by ▴ 50 • written 8.6 years ago by • 0
4
votes
9
replies
3.1k
views
Limma is doing the right way to calculate the fold change?
limma proteomics
updated 8.6 years ago by 1.6k • written 8.6 years ago by ▴ 30
0
votes
4
replies
3.0k
views
Gviz : sort reads in AlignmentsTracks and display reads containing indels
gviz
updated 8.6 years ago by ★ 1.6k • written 8.7 years ago by • 0
1
vote
3
replies
1.5k
views
find fold change in DESeq2 results
deseq2
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 100
2
votes
3
replies
3.3k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq deseq2 tximport salmon normalization
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
0
votes
2
replies
1.8k
views
WGCNA: error message in blockwiseModule(): address 0x0, cause 'memory not mapped'
wgcna
updated 8.6 years ago by ★ 3.0k • written 8.6 years ago by • 0
0
votes
1
reply
1.4k
views
trackviewer lolliplot pie.stack
lolliplot trackviewer
updated 8.6 years ago by ★ 1.3k • written 8.6 years ago by • 0
0
votes
0
replies
1.1k
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
8.6 years ago rezapanahi222 • 0
0
votes
1
reply
1.5k
views
DiffBind error Error in pv.getPlotData
DiffBind
updated 8.6 years ago by ★ 5.2k • written 8.6 years ago by ▴ 10
46,716 results • Page 327 of 935
Recent ...
Replies
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 10
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…
Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k
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…
Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Comment: Opportunity to host EuroBioC2026 Preconference workshops! by TikTsokaas33ocissalpc • 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
A: Conversion from counts to FPKM
Answer: Incosistencies in buildSNNGraph() function
Awards • All
Great Question to fl ▴ 20
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
Popular Question to Hervé Pagès 16k
Locations • All
United States, 2 minutes ago
United States, 16 minutes ago
United States, 49 minutes ago
Australia, 58 minutes ago
Australia/Melbourne, 1 hour ago
Traffic: 1478 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