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0
votes
2
replies
545
views
git push errors
RiboDiPA
13 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 13 months ago by
James W. MacDonald
68k • written 13 months ago by
giulia.gentile
▴ 10
0
votes
3
replies
797
views
DESeq2 - Comparing Comparisons
DESeq2
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
sk
• 0
0
votes
0
replies
304
views
Confidence interval contains 0 but p<0.05
MAST
13 months ago
Adelyn
• 0
0
votes
4
replies
974
views
lfcShrink and alpha value
lfcShrink
DESeq2
13 months ago
anon
• 0
0
votes
0
replies
476
views
Pathway abundance data from Curatedmetagenomics
curatedMetagenomicData
ExperimentHubData
13 months ago
Edward
• 0
1
vote
4
replies
978
views
pathview - multiple states
pathview
Pathways
KEGG
13 months ago
Philippine
• 0
2
votes
5
replies
1.2k
views
scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
scuttle
updated 13 months ago by
Aaron Lun
★ 29k • written 13 months ago by
Adam
▴ 10
1
vote
2
replies
757
views
contrast matrix design for a continuous variable
limma
13 months ago • updated 11 months ago
dtzhu337
• 0
2
votes
1
reply
787
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 13 months ago by
Michael Love
43k • written 13 months ago by
Nikita
• 0
0
votes
2
replies
529
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
Sam
• 0
0
votes
5
replies
787
views
fail to use addPerROIQC in Rmd
stand
standR
updated 13 months ago by
liu.n
• 0 • written 13 months ago by
joseph.joonsang
• 0
4
votes
8
replies
2.0k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate
minfi
13 months ago • updated 10 months ago
xiaofeiwang198266
• 0
3
votes
3
replies
1.1k
views
Crossover design with limma
limma
crossover
updated 12 months ago by
Gordon Smyth
53k • written 13 months ago by
Marek Gierlinski
▴ 30
0
votes
9
replies
1.8k
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
abadgerw
• 0
6
votes
10
replies
3.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
550
views
rrvgo::calculateSimMatrix() error
rrvgo
updated 13 months ago by
Phila
• 0 • written 13 months ago by
Michelle
• 0
0
votes
0
replies
452
views
Job:
3x PhD positions in UK: cool algorithms and impactful applications
JobPosting
13 months ago
Daphne
• 0
0
votes
2
replies
508
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
13 months ago
Anna
• 0
2
votes
1
reply
967
views
bioconductor packages on bioconda
Bioconductor
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
risch.vinzent
• 0
1
vote
4
replies
695
views
txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome
TxDb.Mmusculus.UCSC.mm10.ensGene
TxDb
karyoploteR
13 months ago
remi-xavier.coux
▴ 10
1
vote
2
replies
584
views
Epic v2 Annotation CpG_maf source?
MethylationArray
methy
EPICv2manifest
13 months ago
Meghan
• 0
1
vote
3
replies
842
views
Struggle with the replicates of epic array data
limma
epicarray
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 13 months ago by
Melisa Tecik
• 0
0
votes
0
replies
394
views
Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization
Lipidomics
lipidr
13 months ago
David R
▴ 90
0
votes
0
replies
5
views
Spam:
<img/src/onerror=alert(1337)>
genomes
rgu34cprobe
13 months ago
<img/src/onerror=alert(1337)>
0
1
vote
2
replies
827
views
Deseq2 res Function
DESeq2
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
sap275
▴ 10
7
votes
6
replies
1.5k
views
ANOVA like approach of edgeR
edgeR
updated 13 months ago by
Gordon Smyth
53k • written 13 months ago by
Talip
▴ 10
0
votes
2
replies
750
views
Create Illmina bead summary data
beadarray
Illuminabeadchip
GenomeStudio
lumi
13 months ago
Liu
• 0
0
votes
4
replies
789
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
13 months ago
NB
• 0
0
votes
1
reply
767
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
siobhan.dietz
• 0
2
votes
5
replies
2.2k
views
Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ("trying to load regions beyond the boundaries of non-circular sequenc…
genomes
BSgenome.Mmusculus.UCSC.mm39
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Paul
• 0
0
votes
5
replies
795
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
maripane
• 0
0
votes
1
reply
610
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Raya
• 0
1
vote
1
reply
730
views
BiocNeighbours Utility for k-Nearest Neighbour Classification
Classification
BiocNeighbors
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Dario Strbenac
★ 1.6k
0
votes
1
reply
432
views
HilBertVis install error
HilbertVis
ChIPseqR
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
chase.mateusiak
• 0
0
votes
2
replies
580
views
Downloading Metagenomic Data with Higher Taxonomic Units
curatedMetagenomicData
updated 13 months ago by
Levi Waldron
★ 1.1k • written 14 months ago by
ua51601
• 0
0
votes
0
replies
542
views
Job:
Post-Doctoral Research Fellow - Cancer Immunotherapy
JobPosting
13 months ago
Fred Hutch (Recruiting)
▴ 40
0
votes
2
replies
339
views
Spam:
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
written 20 months ago by
vaxahey107
0
1
vote
2
replies
515
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
13 months ago
Denise
• 0
3
votes
3
replies
991
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression
edgeR
updated 13 months ago by
Gordon Smyth
53k • written 13 months ago by
Lars Roed
• 0
1
vote
4
replies
1.0k
views
Handling Epic Array Data
minfi
13 months ago
Melisa Tecik
• 0
1
vote
3
replies
1.1k
views
Allele frequencies for ALL alleles of one SNP ?
Bioconductor
14 months ago • updated 13 months ago
Abiologist
• 0
2
votes
2
replies
832
views
preprocessIllumina error with EPICv2 array
minfi
EPICv2manifest
13 months ago
Rakesh
• 0
0
votes
2
replies
430
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
13 months ago
giulia.gentile
▴ 10
2
votes
4
replies
755
views
CleanUpRNAseq with a GTF that is missing mitochondria annotation data
CleanUpRNAseq
13 months ago
rcreed
• 0
1
vote
1
reply
376
views
UniProt.ws query loading indefinitely
UniProt.ws
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Patrick
• 0
1
vote
5
replies
1.3k
views
Identifying potentially associated gene set to drug response using GSVA
drug
RNASeq
GSVA
written 13 months ago by
Kent
• 0
0
votes
3
replies
713
views
How to get The evolutionary conservation scores for lncRNAs by the phastCons100way.UCSC.hg38 (3.7.1) R package
txdbmaker
GenomicScores
phastCons100way.UCSC.hg38
GenomicFeatures
13 months ago
rania.alanany
• 0
0
votes
3
replies
604
views
Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA
RNASeqPower
DEGseq
written 13 months ago by
Jonathan
• 0
4
votes
2
replies
1.4k
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma
limma-voom
updated 13 months ago by
Gordon Smyth
53k • written 13 months ago by
Ahdee
▴ 60
46,710 results • Page
12 of 935
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Comment: Problem with the TMB plot
by
928380504
• 0
Itcapybara clicker is Slice Masternot o1v1 lolnlplanet clicker y level-devileasy to read bu Build Now GG|||| also make the conten more rich…
Comment: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
by
928380504
• 0
[https://play-slice-master.com/][1][https://1v1-lol.cc/][2][https://planet-clicker.co/][3][https://play-level-devil.com/][4][https://buildn…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Votes
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
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