Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
2
votes
2
replies
1.8k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
21 months ago
Eva
▴ 10
0
votes
4
replies
1.1k
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
21 months ago • updated 20 months ago
Efra
• 0
1
vote
1
reply
716
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Emma
• 0
0
votes
1
reply
452
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 21 months ago by
Michael Love
43k • written 21 months ago by
rahaf.nazzal9
• 0
0
votes
1
reply
1.6k
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Yuqin
• 0
3
votes
9
replies
8.2k
views
enrichGOgradient color change
clusterProfiler
updated 11 months ago by
lewis.roper
• 0 • written 2.1 years ago by
inna.gur
• 0
1
vote
5
replies
1.4k
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
21 months ago
Gerhard Thallinger
▴ 180
5
votes
7
replies
1.6k
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 20 months ago by
Gordon Smyth
53k • written 21 months ago by
Amit
• 0
0
votes
2
replies
886
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
z_bahari
• 0
1
vote
1
reply
1.4k
views
Perfoming clumping using ieugwasr package
LinkageDisequilibrium
genom
linka
GenomicDistributionsData
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
zoheir.alayash
▴ 10
2
votes
2
replies
783
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
21 months ago
feather-W
• 0
0
votes
1
reply
696
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Gerhard Thallinger
▴ 180
2
votes
2
replies
963
views
between lane normalization upper quantile
EDASeq
edgeR
21 months ago
elesofi
• 0
2
votes
3
replies
3.6k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 21 months ago by
ATpoint
★ 5.0k • written 3.7 years ago by
liqidong52
▴ 20
0
votes
1
reply
700
views
problem with ClusterRepro function
WGCNA
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Antonio.Aubry
• 0
0
votes
2
replies
1.2k
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 21 months ago by
Michael Love
43k • written 21 months ago by
gglatzer
• 0
0
votes
4
replies
888
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Jad
• 0
2
votes
2
replies
863
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
21 months ago
Sabiha
▴ 20
0
votes
10
replies
1.7k
views
DESeq2 filtering vs edgeR filtering
DESeq2
written 21 months ago by
fr8712ca-s
• 0
0
votes
2
replies
940
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
21 months ago
Sam
▴ 10
0
votes
2
replies
3.1k
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
21 months ago
kcarey
• 0
1
vote
1
reply
602
views
i'm not getting any differentially expressed genes.
DESeq2
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Marilyn
• 0
2
votes
1
reply
826
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
hemantcnaik
• 0
0
votes
1
reply
783
views
Exact same results in Diffbind with different normalization methods
DiffBind
21 months ago
red_bricks
▴ 60
0
votes
0
replies
549
views
FELLA plotGraph function won't change the legend
FELLA
21 months ago
yuhang
• 0
0
votes
0
replies
479
views
medips-output
ngsReports
MEDIPS
21 months ago
Researcher
▴ 10
1
vote
1
reply
786
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
updated 7 weeks ago by
teamardigen
• 0 • written 21 months ago by
bocsci11
▴ 10
0
votes
1
reply
612
views
Syntenet error in infer_syntenet() Error in blast_list[[1]] : subscript out of bounds
syntenet
updated 21 months ago by
Fabricio Almeida-Silva
▴ 40 • written 22 months ago by
Sujeevan
• 0
0
votes
1
reply
696
views
question about data processing for syntenet
syntenet
updated 21 months ago by
Fabricio Almeida-Silva
▴ 40 • written 23 months ago by
Sujeevan
• 0
0
votes
4
replies
779
views
Error in classify_gene_pairs
syntenet
doubletrouble
21 months ago
hfyuan2016
• 0
2
votes
1
reply
752
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
maltethodberg
▴ 180
0
votes
0
replies
418
views
The graphical interface of FELLA doesn't work
FELLA
21 months ago
yuhang
• 0
0
votes
0
replies
500
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
21 months ago
jean-christophe.helbling
• 0
1
vote
1
reply
525
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
synat.keam
• 0
1
vote
3
replies
1.0k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 22 months ago by
pl23
• 0
0
votes
2
replies
965
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
21 months ago
Viktor Thiel
• 0
0
votes
0
replies
648
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
21 months ago
Henry
• 0
0
votes
1
reply
1.2k
views
Rcpp compilation error
Release
Rcpp
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Robert K. Bradley
▴ 40
0
votes
1
reply
805
views
Rain error: invalid annotation of time points
rain
updated 10 months ago by
Dominik
• 0 • written 21 months ago by
mpuli011
• 0
0
votes
0
replies
785
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
21 months ago
Felix
• 0
0
votes
1
reply
853
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2
scCITE-seq
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
daiane.hemerichbrennan
• 0
1
vote
2
replies
785
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
21 months ago
thomas
• 0
1
vote
1
reply
622
views
Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
ronin
• 0
0
votes
8
replies
1.6k
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
21 months ago
michelafrancesconi8
• 0
0
votes
1
reply
674
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Sneha
• 0
0
votes
1
reply
723
views
News:
Join BOC Sciences at Drug Discovery Chemistry 2024
DFP
written 21 months ago by
cv.jam.zhxf17875
• 0
2
votes
6
replies
1.6k
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
21 months ago • updated 20 months ago
Lily Cheang
▴ 10
3
votes
8
replies
1.4k
views
Constrast for Time Course Experiments using Limma
limma
21 months ago
dl17032000
• 0
1
vote
4
replies
921
views
DESeq2 Replicates
DESeq2
RNASeq
21 months ago
kcarey
• 0
2
votes
6
replies
1.0k
views
Factor vs Character in design
DESeq2
21 months ago
James Aiden
• 0
46,692 results • Page
29 of 934
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards
• All
Popular Question
to
shepherl
4.2k
Popular Question
to
James W. MacDonald
68k
Popular Question
to
Gordon Smyth
53k
Commentator
to
sina.nassiri
▴ 130
Popular Question
to
Hervé Pagès
16k
Locations
• All
United States,
53 minutes ago
Seattle, WA, United States,
56 minutes ago
Uzbekistan,
1 hour ago
United States,
1 hour ago
WEHI, Melbourne, Australia,
2 hours ago
Traffic: 2334 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