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0
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29
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
updated 1 hour ago by
ATpoint
★ 4.6k • written 17 hours ago by
Kucsera
• 0
0
votes
0
replies
42
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
2 days ago
KR
• 0
0
votes
1
reply
85
views
combining raw counts and estimated counts
RNASeqData
GEO
TCGAbiolinks
updated 3 days ago by
O'Brien
• 0 • written 5 days ago by
Noor
• 0
0
votes
0
replies
70
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR
DESeq2
5 days ago
Jimmy Mak
• 0
0
votes
2
replies
1.0k
views
News:
EuroBioC2023 abstract submission closing soon!
presentation
EuroBioc2023
Conference
community
Bioconductor
updated 5 days ago by
excess.gecko.shso
• 0 • written 20 months ago by
Maria Doyle
▴ 90
0
votes
5
replies
1.1k
views
News:
EuroBioC2024 abstract submission is open!
Conference
Bioconductor
EuroBioC2024
updated 2 days ago by
Alan Downey
• 0 • written 10 months ago by
Maria Doyle
▴ 90
0
votes
2
replies
386
views
Cross-validation with multiple control subgroups in limma
limma
multtest
8 days ago • updated 7 days ago
Ali Barry
▴ 40
1
vote
1
reply
217
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 9 days ago by
Michael Love
43k • written 18 days ago by
txema.heredia
• 0
0
votes
0
replies
55
views
Job:
Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal Patterning
JobPosting
10 days ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
201
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 3 days ago by
O'Brien
• 0 • written 10 days ago by
André
• 0
4
votes
8
replies
1.1k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker
GenomeInfoDb
GenomicFeatures
Biostrings
gDNAx
updated 8 days ago by
Robert Castelo
★ 3.4k • written 11 days ago by
rohitsatyam102
▴ 20
1
vote
9
replies
716
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 11 days ago by
anna.cot.anna.cot
▴ 30
0
votes
2
replies
141
views
Error in get_anno_data(ontology) : ontology not supported yet...
EnrichDO
11 days ago
GODseeker
• 0
0
votes
2
replies
250
views
Standardization of rlog transformed counts before PCA
RNASeq
DESeq2
Visualization
updated 12 days ago by
ATpoint
★ 4.6k • written 16 days ago by
bbao
• 0
0
votes
2
replies
211
views
Build error on kunpeng2 Linux aarch64
Bioconductor
updated 12 days ago by
martin.grigorov
▴ 10 • written 13 days ago by
Hongxiang
• 0
0
votes
3
replies
1.3k
views
Limma - using both array and spot weights in lmFit
Genetics
Genetics
written 17.7 years ago by
Jakob Hedegaard
▴ 170
0
votes
2
replies
415
views
Margins for gene_set_enrichment_plot
spatialLIBD
updated 15 days ago by
Leonardo Collado Torres
★ 1.1k • written 21 days ago by
Oliver
• 0
0
votes
1
reply
131
views
Errors running learn.bn function from Pigengene in windows environment
Pigengene
written 15 days ago by
Thomas
• 0
0
votes
1
reply
227
views
Need new version : tx2gene.gencode.v47.csv
tximportData
updated 16 days ago by
Guido Hooiveld
★ 4.1k • written 16 days ago by
gauravbcbp22
• 0
1
vote
5
replies
465
views
Deseq2 Design
RNASeq
DESeq2
updated 12 days ago by
James W. MacDonald
67k • written 16 days ago by
pm_25
• 0
0
votes
5
replies
416
views
p value is 0, padj is 0
DESeq2
17 days ago • updated 16 days ago
Wirayatida
• 0
0
votes
2
replies
366
views
Cannot install GO.db and org.Hs.eg.db
Install
updated 17 days ago by
James W. MacDonald
67k • written 17 days ago by
Gabriel
• 0
0
votes
5
replies
535
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 17 days ago by
Aichatou
• 0
4
votes
8
replies
981
views
Feature Counts - potential bug with outfile.jcounts
featurecounts
Rsubread
19 days ago • updated 11 days ago
chris2.a.white
• 0
1
vote
2
replies
419
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
18 days ago • updated 17 days ago
georgii.vdovin
• 0
0
votes
1
reply
483
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
updated 17 days ago by
Gordon Smyth
52k • written 10 months ago by
chris2.a.white
• 0
0
votes
0
replies
10
views
Spam:
Best Hotels In Maui
prebs
18 days ago
2zrcj3448p
0
0
votes
1
reply
8
views
Spam:
Small Business Directory Emerald Coast
BUScorrect
offtopic
updated 18 days ago by
shepherl
4.1k • written 18 days ago by
2zrcj3448p
0
6
votes
5
replies
1.8k
views
MEDIPS for chIP-Seq
ChIPSeq
written 2.4 years ago by
Darek
▴ 30
0
votes
1
reply
133
views
Matching patterns in an AAStringset
Biostrings
updated 18 days ago by
Aidan
▴ 60 • written 19 days ago by
Cédric
• 0
0
votes
2
replies
269
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
19 days ago • updated 18 days ago
Tadeoye
▴ 20
0
votes
7
replies
699
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 18 days ago by
txema.heredia
• 0 • written 20 days ago by
fjrsa
• 0
2
votes
4
replies
399
views
Can we get beta values with DMRcate package
DMRcatedata
DMRcate
20 days ago • updated 18 days ago
Melisa Tecik
• 0
2
votes
2
replies
319
views
Running multiple KNN queries in parallel
BiocParallel
BiocNeighbors
23 days ago • updated 21 days ago
SamGG
▴ 360
5
votes
4
replies
681
views
RSubread output significantly different from bash Subread output
Subread
Rsubread
updated 19 days ago by
ATpoint
★ 4.6k • written 22 days ago by
Aimee
• 0
0
votes
0
replies
87
views
Job:
Postdoc/Staff Scientist Position at UT Southwestern Medical Center
PathologyData
LungCancerData
JobPosting
21 days ago
cailing20
• 0
0
votes
1
reply
239
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 22 days ago by
Michael Love
43k • written 22 days ago by
bhandary.8590
▴ 20
0
votes
2
replies
443
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 22 days ago by
Gordon Smyth
52k • written 23 days ago by
Lina
▴ 10
0
votes
2
replies
209
views
git push errors
RiboDiPA
23 days ago
Jiping Wang
▴ 90
2
votes
3
replies
1.2k
views
How to annotate a limma Elist raw class object with an annotation file
limma
AnnotationDbi
updated 24 days ago by
James W. MacDonald
67k • written 25 days ago by
giulia.gentile
▴ 10
0
votes
3
replies
348
views
DESeq2 - Comparing Comparisons
DESeq2
updated 17 days ago by
James W. MacDonald
67k • written 24 days ago by
sk
• 0
0
votes
0
replies
89
views
Confidence interval contains 0 but p<0.05
MAST
24 days ago
Adelyn
• 0
0
votes
4
replies
473
views
lfcShrink and alpha value
lfcShrink
DESeq2
4 weeks ago • updated 24 days ago
cropero
• 0
0
votes
0
replies
83
views
Pathway abundance data from Curatedmetagenomics
curatedMetagenomicData
ExperimentHubData
25 days ago
Edward
• 0
1
vote
4
replies
333
views
pathview - multiple states
pathview
Pathways
KEGG
25 days ago
Philippine
• 0
2
votes
5
replies
633
views
scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
scuttle
updated 24 days ago by
Aaron Lun
★ 28k • written 26 days ago by
Adam
▴ 10
1
vote
2
replies
305
views
contrast matrix design for a continuous variable
limma
26 days ago
dtzhu337
• 0
1
vote
1
reply
239
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 26 days ago by
Michael Love
43k • written 4 weeks ago by
Nikita
• 0
0
votes
2
replies
170
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates
DESeq2
updated 26 days ago by
Michael Love
43k • written 27 days ago by
Sam
• 0
0
votes
5
replies
341
views
fail to use addPerROIQC in Rmd
stand
standR
updated 26 days ago by
liu.n
• 0 • written 27 days ago by
joseph.joonsang
• 0
46,255 results • Page
1 of 926
Recent ...
Replies
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character
by
ATpoint
★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format
by
ControlF5
• 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open!
by
Alan Downey
• 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
by
O'Brien
• 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts
by
O'Brien
• 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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