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Interpretation of GSVA with absRanking=TRUE
GSVA
18 months ago
gad.abraham
• 0
0
votes
1
reply
742
views
Can we compare 3 different experimental conditions with DESeq2?
DESeq2
StatisticalMethod
updated 18 months ago by
swbarnes2
★ 1.4k • written 18 months ago by
Esteban
• 0
0
votes
1
reply
660
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData
DESeq2
DifferentialExpression
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
ZhuYi
• 0
1
vote
2
replies
2.9k
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using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 18 months ago by
rodrigo.duarte88
▴ 40 • written 6.2 years ago by
mohamedrefaat.1.1992
• 0
0
votes
1
reply
547
views
How to access the Bioconductor in Windows
Bioconductor
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
fahad.rashid
• 0
0
votes
3
replies
909
views
STRINGdb server response time for mapping
mapping
serverresponsetime
STRINGdb
updated 18 months ago by
damian.szk
▴ 110 • written 18 months ago by
roberto.pellegrino
• 0
3
votes
6
replies
1.4k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
18 months ago
JG13
• 0
0
votes
0
replies
870
views
Job:
Group Leader (Faculty) positions at EMBL-EBI, Cambridge UK
research
exciting
career
escape
18 months ago
Wolfgang Huber
★ 13k
1
vote
3
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964
views
STRINGdb v.2.16.4 does not render the plot [libpng error: Not a PNG file]
STRINGdb
updated 18 months ago by
damian.szk
▴ 110 • written 18 months ago by
h.valipour.k
• 0
0
votes
4
replies
920
views
Add mask to BSgenome
Mask
BSgenome.Hsapiens.UCSC.hg38.masked
19 months ago • updated 18 months ago
shraddha.pai
• 0
0
votes
0
replies
442
views
does TMixClust recognise biological replicates
TMixClust
19 months ago
ta_awwad
▴ 10
0
votes
1
reply
539
views
multiple condition issue running DESeq
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
Kelly
• 0
0
votes
4
replies
1.0k
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
19 months ago
JG13
• 0
2
votes
2
replies
914
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 19 months ago by
jessica.anderson
▴ 10 • written 19 months ago by
Đình Vinh
• 0
2
votes
2
replies
1.1k
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 19 months ago by
jessica.anderson
▴ 10 • written 19 months ago by
ttt
• 0
1
vote
2
replies
2.0k
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How to compare subset of samples from VCF files
VCF
VariantAnnotation
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
Marco
• 0
0
votes
3
replies
770
views
Ploting of normalized counts after batch removal
DESeq2
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
altuda
▴ 10
0
votes
0
replies
866
views
How to fix fix $PnR in flowCore
flowCore
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Elle
• 0
1
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1
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1.5k
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News:
Win 1 of 50 free virtual registrations to BioC Asia 2022 (Dec 1-2, 2022)
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written 3.1 years ago by
Peter Hickey
▴ 760
0
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0
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472
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Error in xj[i] : invalid subscript type 'list' when running jDUreport on Aspli
ASpli
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Randall
• 0
0
votes
3
replies
996
views
Gviz and custom database
Gviz
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
luigi.faino
• 0
1
vote
1
reply
507
views
makeExampleDESeqDataSet using pilot data
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
li.d.peck
• 0
0
votes
0
replies
526
views
EuroBioC2024 Registration is Open!
Community
Conference
Bioconductor
EuroBioC2024
19 months ago
Maria Doyle
▴ 110
0
votes
2
replies
703
views
Best way to describe DEseq2 design
DESeq2
updated 19 months ago by
swbarnes2
★ 1.4k • written 19 months ago by
YouCook
• 0
2
votes
3
replies
1.9k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 19 months ago by
Hervé Pagès
16k • written 19 months ago by
Ali Osman
• 0
0
votes
0
replies
456
views
Message 'invalid data format' on impute.MAR function
impute
19 months ago
marcosdossantosferreira
• 0
0
votes
1
reply
1.3k
views
scds creates sparse->dense coercion
scds
19 months ago • updated 17 months ago
Lluís Revilla Sancho
▴ 760
1
vote
2
replies
846
views
Deseq2
DESeq2
rnaseqGene
updated 19 months ago by
Ram
▴ 220 • written 19 months ago by
Sudip
• 0
0
votes
0
replies
409
views
Import_picrust2 question
microbiomeMarker
19 months ago
Jay
• 0
0
votes
1
reply
975
views
Error in render R qmd document (could not find function "process")
quantro
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Chutian
• 0
0
votes
0
replies
841
views
Job:
Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell
Transcriptomics
SpatialDatasets
SpatialData
19 months ago
Silvio
• 0
1
vote
1
reply
586
views
LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
boczniak767
▴ 740
0
votes
6
replies
1.2k
views
Counter-directional LFC shrinkage
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
ennui
• 0
0
votes
3
replies
1.9k
views
ChAMP not available for bioconductor 3.19
Bioconductor
ChAMP
updated 19 months ago by
shepherl
4.2k • written 19 months ago by
Macsue
• 0
1
vote
4
replies
1.6k
views
Error in gseDO function
DOSE
gsea
19 months ago
Javier
• 0
0
votes
0
replies
482
views
gmapR source package contains x86_64 binaries
gmapR
19 months ago
Tom Lin
• 0
0
votes
0
replies
25
views
Spam:
Drug Discovery
flowBeads
19 months ago
Zoe
0
0
votes
2
replies
1.3k
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
DESeq2
single-cell
scRNA
Pseudobulk
updated 19 months ago by
Guido Hooiveld
★ 4.1k • written 19 months ago by
Sara
• 0
1
vote
2
replies
985
views
conumee with Infinium MethylationEPIC v2.0
conumee
written 19 months ago by
Maximus
▴ 10
0
votes
3
replies
2.1k
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 19 months ago by
Robert Castelo
★ 3.4k • written 19 months ago by
michelafrancesconi8
• 0
0
votes
0
replies
587
views
News:
Legacy Bioconductor Installation
Installation
Bioconductor
19 months ago
shepherl
4.2k
1
vote
9
replies
2.0k
views
Cannot install oligo on Fedora
oligo
source
Install
19 months ago • updated 18 months ago
Guido Hooiveld
★ 4.1k
0
votes
5
replies
1.2k
views
Error when running topGO with KS statistic and elim agorithm
topGO
19 months ago • updated 18 months ago
A. denDekker
• 0
0
votes
2
replies
1.3k
views
Cluster columns in Pheatmap
geneexp
pheatmap
heatmaps
cluster
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
pehove2385
• 0
0
votes
2
replies
1.0k
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2
clinicaltraits
Normalization
batchnormalisation
19 months ago
sukeshinik5
▴ 20
0
votes
0
replies
682
views
News:
Online course: Network Analysis in Systems Biology with R/Bioconductor
SystemsBiology
Bioconductor
Network
19 months ago
info
▴ 10
0
votes
4
replies
2.2k
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
tjl
• 0
0
votes
1
reply
596
views
News:
Bioconductor Build System
Builds
Bioconductor
written 19 months ago by
shepherl
4.2k
8
votes
6
replies
9.2k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler
enrichplot
updated 19 months ago by
jovel_juan
▴ 30 • written 6.6 years ago by
charles.foster
▴ 180
0
votes
0
replies
667
views
News:
BioC2024 Bioconductor Carpentries RNA-Seq Workshop July 22-23
BioC2024
Conference
Bioconductor
Community
19 months ago
Maria Doyle
▴ 110
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Comment: nice 3D displays for PCA analysis
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adam80haynes
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That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital
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TikTsokaasocissalpc
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The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
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If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Answer: Limma-voom sample weights and impact on DEG numbers
by
Gordon Smyth
53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Answer: wgcna module preseravtion taking too long?
by
ATpoint
★ 5.0k
WGCNA is not a Bioconductor package, you won't get an answer here. Consider biostars.org or the r/bioinformatics reddit. Note that 10 sampl…
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Limma-voom sample weights and impact on DEG numbers
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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
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