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
0
votes
3
replies
1.5k
views
problem for finding soft power for constructing network in WGCNA algorithm
RNA-seq
WGCNA package
soft power
written 7.4 years ago by
modarzi
▴ 10
0
votes
6
replies
505
views
GO.db and others package Download failure
GO.db
Bioconductor
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
Skyler
• 0
0
votes
0
replies
7
views
Spam:
Best Rehab Center In India | Luxury, Alcohol & Mental Health Care
COSMIC.67
3 months ago
Best Rehab Center
0
2
votes
2
replies
302
views
replace cat with message in glmTreat when lfc = 0
edgeR
glmTreat
updated 3 months ago by
Gordon Smyth
53k • written 3 months ago by
oliverd
• 0
0
votes
1
reply
204
views
Job:
Research and Service Group Leader positions in AI in Biology at EMBL
Bioconductor
written 3 months ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
178
views
Differential motif analysis
motifmatchr
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
Marek Gierlinski
▴ 30
0
votes
1
reply
226
views
News:
Ensembl 115 has been released!
ensembl
ensembldb
biomaRt
written 3 months ago by
Ensembl_Jorge
▴ 10
1
vote
3
replies
427
views
readDNAStringSet with non DNA characters
Biostrings
3 months ago
biomiha
▴ 20
0
votes
2
replies
280
views
readBam vs read_bam_insert_metrics
cfDNAPro
cfDNA
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
rtrivedi1
▴ 10
1
vote
3
replies
419
views
How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?
BSgenome
BSgenomeForge
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
mat149
▴ 80
3
votes
14
replies
1.2k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 4 months ago by
Aurélie
• 0
5
votes
13
replies
1.3k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma
RNASeq
scRNAseq
updated 12 weeks ago by
Gordon Smyth
53k • written 3 months ago by
abaed
• 0
0
votes
1
reply
3.2k
views
Job:
Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer
computational biology
rnaseq
chipseq
Job
written 11.1 years ago by
gcyuan
• 0
0
votes
3
replies
376
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
yongjie.wang
• 0
0
votes
1
reply
707
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
KS
• 0
0
votes
3
replies
258
views
A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::select()
org.Ss.eg.db
AnnotationDbi
written 3 months ago by
Adam Munhall
• 0
0
votes
4
replies
439
views
voomLmFit fitted log-CPM values
limma
edgeR
updated 3 months ago by
Gordon Smyth
53k • written 3 months ago by
Lina
▴ 10
1
vote
3
replies
378
views
ROAST compare results with complex design
limma
mroast
roast
CAMERA
written 3 months ago by
Jiahao Tian
• 0
0
votes
0
replies
6
views
Spam:
Exploring Robotic Hair Restoration Procedure
COSMIC.67
3 months ago
paseje6172
0
0
votes
0
replies
156
views
News:
Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment
SingleCell
SingleCellWorkflow
SingleCellData
3 months ago
Ludwig Geistlinger
▴ 70
3
votes
5
replies
1.1k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
snijesh
▴ 200
0
votes
1
reply
384
views
News:
Bioconductor Board Nominations Open
TAB
Bioconductor
CAB
written 5 months ago by
shepherl
4.2k
2
votes
8
replies
750
views
Are voomByGroup and voomLmFit compatible?
limma
voomLmFit
voomByGroup
updated 3 months ago by
Gordon Smyth
53k • written 4 months ago by
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
1.3k
views
How to analyze Affy data, CEL files not available
affy
affy
written 18.9 years ago by
Bobby Prill
▴ 60
0
votes
5
replies
650
views
HMP_2019_t2d data origin
curatedMetagenomicData
updated 3 months ago by
Levi Waldron
★ 1.1k • written 5 months ago by
Blan
• 0
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 3 months ago by
James W. MacDonald
68k • written 6.4 years ago by
lim6432
▴ 60
3
votes
4
replies
8.1k
views
Calculation of module membership in WGCNA
WGCNA
RNA-seq
ModuleMembership
Network
Hub gene
written 5.4 years ago by
Arindam
▴ 80
0
votes
11
replies
674
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
4 months ago • updated 3 months ago
Denise
• 0
3
votes
4
replies
543
views
p-adjusted values in multiple comparisons
StatisticalMethod
limma
RnaSeqSampleSizeData
updated 3 months ago by
Josh
• 0 • written 4 months ago by
ocanorocabayera
• 0
2
votes
6
replies
607
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
4 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
296
views
DESeq2 inconsistent fits depending on model design with interacting factors
des
DESeq2
written 4 months ago by
fedor.bezrukov
▴ 10
0
votes
2
replies
642
views
Job:
Job: Ensembl Genebuild Project Leader
JobPosting
ensembldb
written 6 months ago by
Aleena_Ensembl
▴ 30
1
vote
2
replies
279
views
The default value of 'abundanceCol'
tximportData
4 months ago
Jinghua
• 0
1
vote
2
replies
363
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
Noah
• 0
2
votes
9
replies
998
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq
edgeR
LongRead
Transcript
4 months ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
389
views
Difference between logFC in limma-voom and weighted limma-voom
limma
voom
weighting
4 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
11
replies
956
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn
10x
scRNAseq
emptyDrops
DropletUtils
4 months ago
Peter Hickey
▴ 760
0
votes
0
replies
6
views
Spam:
Chat GPT Gratuit
chipenrich
procoil
4 months ago
Lệ
0
3
votes
1
reply
388
views
Limpa Pipeline Order
limma
limpa
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
abadgerw
• 0
3
votes
2
replies
458
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
A.Barden
▴ 10
0
votes
8
replies
654
views
How to use limma to analyze complex temporal RNAseq data
timecourse
RNASeq
limma
4 months ago
Jiahao Tian
• 0
3
votes
7
replies
754
views
makeChipPackage(): Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows:
AnnotationForge
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Jaqueline
• 0
2
votes
2
replies
427
views
Limma : paired samples leading to unexpected estimates
limma
4 months ago
Basti
▴ 780
2
votes
2
replies
524
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
4 months ago
sandmann.t
▴ 70
0
votes
1
reply
207
views
muffz.plot2
Mfuzz
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
xiao
• 0
0
votes
4
replies
894
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm
s-value
DESeq2
updated 4 months ago by
Michael Love
43k • written 5 months ago by
Erika
• 0
1
vote
2
replies
418
views
Differential expression on the transcript-level
DESeq2
updated 4 months ago by
swbarnes2
★ 1.4k • written 4 months ago by
泓朴
• 0
0
votes
3
replies
566
views
DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
4 months ago
Shajahan
• 0
3
votes
13
replies
2.2k
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 14 months ago by
bioshot.com
• 0
3
votes
2
replies
913
views
Transcript expression analysis using EdgeR
edgeR
Transcript
RNASeq
4 months ago
mohammedtoufiq91
▴ 10
46,696 results • Page
3 of 934
Recent ...
Replies
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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…
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
Dario Strbenac
★ 1.6k
Scholar
to
Nikos Ignatiadis
▴ 180
Popular Question
to
Robert
• 0
Popular Question
to
lamia11me
• 0
Popular Question
to
Gordon Smyth
53k
Locations
• All
USA,
1 minute ago
Italy,
44 minutes ago
The city by the bay,
1 hour ago
Poland,
1 hour ago
United States,
4 hours ago
Traffic: 1236 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