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0
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482
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Correlation between gene clusters
genomes
RNASeqData
written 11 months ago by
Le
• 0
0
votes
2
replies
737
views
Mean variance curve troubleshoot filtering
limmavoom
filtering
edgeR
RNASeqData
meanvariancetrend
11 months ago
gingergeiger22
• 0
0
votes
1
reply
625
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR
DESeq2
updated 11 months ago by
Michael Love
43k • written 12 months ago by
Jimmy Mak
• 0
2
votes
1
reply
747
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 11 months ago by
Michael Love
43k • written 12 months ago by
KR
• 0
0
votes
1
reply
1.7k
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate
Gviz
updated 11 months ago by
ming
• 0 • written 4.0 years ago by
Ahdee
▴ 60
6
votes
5
replies
1.1k
views
How do I fix an odd voom plot in a combined dataset?
limma
Normalization
voom
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
1sunmic2
• 0
1
vote
8
replies
1.6k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
11 months ago
Andre
• 0
0
votes
2
replies
754
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
12 months ago
Kucsera
• 0
0
votes
1
reply
655
views
combining raw counts and estimated counts
RNASeqData
GEO
TCGAbiolinks
updated 12 months ago by
O'Brien
• 0 • written 12 months ago by
Noor
• 0
0
votes
4
replies
2.3k
views
News:
EuroBioC2023 abstract submission closing soon!
presentation
EuroBioc2023
Conference
community
Bioconductor
written 2.7 years ago by
Maria Doyle
▴ 110
0
votes
2
replies
820
views
Cross-validation with multiple control subgroups in limma
limma
multtest
12 months ago
Ali Barry
▴ 40
1
vote
1
reply
567
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 12 months ago by
Michael Love
43k • written 12 months ago by
txema.heredia
• 0
0
votes
1
reply
601
views
Job:
Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal Patterning
JobPosting
updated 11 months ago by
iqratechnology4
• 0 • written 12 months ago by
Jenny Drnevich
★ 2.0k
0
votes
1
reply
680
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 12 months ago by
O'Brien
• 0 • written 12 months ago by
André
• 0
1
vote
9
replies
1.6k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 12 months ago by
anna.cot.anna.cot
▴ 40
0
votes
2
replies
1.2k
views
Error in get_anno_data(ontology) : ontology not supported yet...
EnrichDO
12 months ago
GODseeker
• 0
4
votes
2
replies
1.1k
views
Standardization of rlog transformed counts before PCA
RNASeq
DESeq2
Visualization
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
bbao
▴ 10
0
votes
2
replies
632
views
Build error on kunpeng2 Linux aarch64
Bioconductor
updated 11 months ago by
wise
• 0 • written 12 months ago by
Hongxiang
• 0
0
votes
3
replies
1.7k
views
Limma - using both array and spot weights in lmFit
Genetics
Genetics
written 18.7 years ago by
Jakob Hedegaard
▴ 170
0
votes
2
replies
707
views
Margins for gene_set_enrichment_plot
spatialLIBD
updated 12 months ago by
Leonardo Collado Torres
★ 1.1k • written 12 months ago by
Oliver
• 0
0
votes
1
reply
316
views
Errors running learn.bn function from Pigengene in windows environment
Pigengene
written 12 months ago by
Thomas
• 0
0
votes
2
replies
862
views
Need new version : tx2gene.gencode.v47.csv
tximportData
12 months ago • updated 6 months ago
Gaurav
• 0
1
vote
5
replies
1.1k
views
Deseq2 Design
RNASeq
DESeq2
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
pm_25
• 0
0
votes
5
replies
1.2k
views
p value is 0, padj is 0
DESeq2
12 months ago
Wirayatida
• 0
0
votes
2
replies
1.8k
views
Cannot install GO.db and org.Hs.eg.db
Install
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
Gabriel
• 0
0
votes
5
replies
1.0k
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 12 months ago by
Aichatou
• 0
1
vote
2
replies
1.2k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
12 months ago
georgii.vdovin
• 0
0
votes
1
reply
898
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
updated 12 months ago by
Gordon Smyth
53k • written 22 months ago by
chris2.a.white
• 0
0
votes
0
replies
10
views
Spam:
Best Hotels In Maui
prebs
12 months ago
2zrcj3448p
0
0
votes
1
reply
9
views
Spam:
Small Business Directory Emerald Coast
BUScorrect
offtopic
updated 12 months ago by
shepherl
4.2k • written 12 months ago by
2zrcj3448p
0
6
votes
5
replies
2.3k
views
MEDIPS for chIP-Seq
ChIPSeq
written 3.4 years ago by
Darek
▴ 30
0
votes
1
reply
406
views
Matching patterns in an AAStringset
Biostrings
updated 12 months ago by
Aidan
▴ 70 • written 12 months ago by
Cédric
• 0
0
votes
2
replies
740
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
12 months ago
Tadeoye
▴ 20
0
votes
7
replies
1.3k
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 12 months ago by
txema.heredia
• 0 • written 12 months ago by
fjrsa
• 0
2
votes
4
replies
934
views
Can we get beta values with DMRcate package
DMRcatedata
DMRcate
12 months ago
Melisa Tecik
• 0
2
votes
2
replies
771
views
Running multiple KNN queries in parallel
BiocParallel
BiocNeighbors
12 months ago
SamGG
▴ 360
5
votes
4
replies
1.4k
views
RSubread output significantly different from bash Subread output
Subread
Rsubread
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
Aimee
▴ 10
0
votes
0
replies
512
views
Job:
Postdoc/Staff Scientist Position at UT Southwestern Medical Center
PathologyData
LungCancerData
JobPosting
12 months ago
cailing20
• 0
0
votes
1
reply
560
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 12 months ago by
Michael Love
43k • written 12 months ago by
bhandary.8590
▴ 20
0
votes
2
replies
958
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 12 months ago by
Gordon Smyth
53k • written 12 months ago by
Lina
▴ 10
0
votes
2
replies
520
views
git push errors
RiboDiPA
12 months ago
Jiping Wang
▴ 90
2
votes
3
replies
1.9k
views
How to annotate a limma Elist raw class object with an annotation file
limma
AnnotationDbi
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
giulia.gentile
▴ 10
0
votes
3
replies
774
views
DESeq2 - Comparing Comparisons
DESeq2
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
sk
• 0
0
votes
0
replies
298
views
Confidence interval contains 0 but p<0.05
MAST
12 months ago
Adelyn
• 0
0
votes
4
replies
950
views
lfcShrink and alpha value
lfcShrink
DESeq2
13 months ago • updated 12 months ago
anon
• 0
0
votes
0
replies
452
views
Pathway abundance data from Curatedmetagenomics
curatedMetagenomicData
ExperimentHubData
12 months ago
Edward
• 0
1
vote
4
replies
954
views
pathview - multiple states
pathview
Pathways
KEGG
12 months ago
Philippine
• 0
2
votes
5
replies
1.1k
views
scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
scuttle
updated 12 months ago by
Aaron Lun
★ 29k • written 12 months ago by
Adam
▴ 10
1
vote
2
replies
743
views
contrast matrix design for a continuous variable
limma
12 months ago • updated 11 months ago
dtzhu337
• 0
2
votes
1
reply
754
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 12 months ago by
Michael Love
43k • written 13 months ago by
Nikita
• 0
1,000 results • Page
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Comment: Ensembl site unresponsive via biomaRt
by
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• 0
Fun, dramatic, and incredibly addictive [Poor Bunny][1] will make you laugh, scream, and keep you glued to the screen. Can you help the poo…
Comment: Limma-voom sample weights and impact on DEG numbers
by
rosarygaseous
• 0
I have faced similar issues before, and often the problem comes down to package versions or R/Bioconductor compatibility. Make sure your R …
Comment: nice 3D displays for PCA analysis
by
adam80haynes
• 0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
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Votes
Limma-voom sample weights and impact on DEG numbers
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
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