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DEseq2
•
reset
0
votes
7
replies
397
views
DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 23 days ago
fr8712ca-s
• 0
13
votes
22
replies
26k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 8 weeks ago by
Michael Love
41k • written 7.8 years ago by
adesrichard
▴ 30
0
votes
11
replies
1.2k
views
Unable to install DESeq2
DESeq2
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
luis.franco
• 0
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 6 months ago by
Michael Love
41k • written 7 months ago by
Christian
• 0
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 8 months ago by
Juan Pablo
• 0 • written 8.3 years ago by
raya.fai
▴ 60
0
votes
4
replies
725
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor
Transcriptomics
DifferentialExpression
DESeq2
11 months ago
sreeshmaraj72
• 0
1
vote
9
replies
5.2k
views
how to control age and gender effect in expression data using DESeq2
deseq2
rnaseq
mirna-seq
differential gene expression
written 6.1 years ago by
klalit1803
• 0
0
votes
3
replies
430
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
4 months ago
Karthik
• 0
1
vote
3
replies
563
views
Read Count Normalisation and validation of analysis
DifferentialExpression
DESeq2
written 3 months ago by
Dinesh
• 0
8
votes
7
replies
1.7k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 9 months ago by
alexandresegers
▴ 20 • written 18 months ago by
jeremymsimon
▴ 20
0
votes
2
replies
1.3k
views
about baseMean in DEseq2
DESeq2
written 2.7 years ago by
Bogdan
▴ 670
0
votes
4
replies
647
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink
DESeq2
written 3 months ago by
Igor
• 0
2
votes
2
replies
286
views
locfunc not found in DESeq2
locfunc
DESeq2
shorth
estimateSizeFactors
7 weeks ago
Hope
▴ 10
0
votes
2
replies
530
views
Heat Map
ColData
pheatmap
DESeq2
written 10 months ago by
dania.khalid
• 0
1
vote
3
replies
436
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 3 months ago by
malliardtee
• 0 • written 4 months ago by
Guangsheng
• 0
0
votes
3
replies
352
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 11 weeks ago by
pl23
• 0
1
vote
3
replies
858
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue
Spati
RSEM
deno
DEseq2
updated 10 months ago by
lauryfriese932
• 0 • written 11 months ago by
shashank
• 0
2
votes
8
replies
1.0k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge
beta
DESeq2
10 months ago
Ndimensional
▴ 20
2
votes
9
replies
1.1k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
9 months ago
Ndimensional
▴ 20
0
votes
4
replies
355
views
Extract LRT results for each comparison
LRT
DESeq2
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
Yijing
• 0
4
votes
9
replies
1.2k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
8 months ago
Luca
• 0
0
votes
2
replies
546
views
DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 4 months ago by
Michael Love
41k • written 4 months ago by
Anonymous Genetics Gnome
• 0
1
vote
5
replies
1.4k
views
How many parameters should be included in the model design for deseq2?
DESeq2
variancePartition
12 months ago • updated 11 months ago
Weiqian
▴ 10
1
vote
8
replies
1.5k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression
DESeq2
written 10 months ago by
sean.mccutcheon
• 0
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 6 months ago by
Hamza
• 0 • written 5.4 years ago by
chiara.facciotto
• 0
0
votes
5
replies
691
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout
DESeq2
written 10 months ago by
Lillian
• 0
3
votes
2
replies
539
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport
DESeq2
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
mckinlee.salazar
• 0
2
votes
6
replies
315
views
Factor vs Character in design
DESeq2
6 weeks ago
James Aiden
• 0
0
votes
17
replies
3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 10 months ago by
snow34
• 0 • written 6.6 years ago by
ap3637
• 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 11 months ago by
informatician
• 0
0
votes
2
replies
604
views
Why my log2fcs are too high?
DESeq2
SingleCell
log2FC
11 months ago
paria.alipour
• 0
0
votes
2
replies
307
views
Complex DESeq2 Experimental Design
DESEq2
DESeq2
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
Elizabeth
• 0
9
votes
5
replies
5.0k
views
Differential expression analysis: Permutation Test
deseq2
limma
edger
permutation
updated 4 months ago by
Gordon Smyth
50k • written 8.2 years ago by
Radek
▴ 90
0
votes
2
replies
318
views
Running DESeq on normalized data
deseq
DESeq2
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
Hugo
• 0
1
vote
3
replies
1.7k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 4.1 years ago by
hasse.bossenbroek
• 0
2
votes
6
replies
2.9k
views
DESeq2 Dispersion Per Condition
deseq2
updated 9 months ago by
adi.rotem
• 0 • written 8.0 years ago by
dsg16
▴ 20
0
votes
3
replies
341
views
LOG2FC DESEQ2
DESeq2
updated 11 weeks ago by
Michael Love
41k • written 11 weeks ago by
ilaria.montali
• 0
5
votes
13
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 39 minutes ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
0
votes
9
replies
2.4k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 5 months ago by
blowfish
• 0 • written 6.5 years ago by
bharata1803
▴ 60
4
votes
7
replies
829
views
weird volcano plot
DESeq2
updated 6 weeks ago by
Shuning
• 0 • written 5 months ago by
shouzheng
▴ 10
0
votes
2
replies
460
views
plotCounts label each sample
p
DESeq2
updated 9 months ago by
ATpoint
★ 4.0k • written 9 months ago by
claire
• 0
1
vote
8
replies
2.7k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.1 years ago by
serpalma.v
▴ 60
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 11 months ago by
ATpoint
★ 4.0k • written 7.7 years ago by
EJ
▴ 20
8
votes
12
replies
2.5k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by
Michael Love
41k • written 11 months ago by
Michael Steinbaugh
▴ 90
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2
lowcount
updated 3 months ago by
Xiao
• 0 • written 9.1 years ago by
aristotele_m
▴ 40
0
votes
5
replies
508
views
Unexpected results for a differential expression analysis between males and females
DESeq2
updated 4 months ago by
Robert Castelo
★ 3.2k • written 4 months ago by
Loïc
• 0
3
votes
6
replies
22k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 3 months ago by
kledo577
• 0 • written 5.6 years ago by
183227851
• 0
0
votes
4
replies
181
views
DEG with low counts
DESeq2
updated 38 minutes ago by
Michael Love
41k • written 4 days ago by
Rajat
• 0
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 21 hours ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
0
votes
2
replies
528
views
Accounting for technical replicates in DESeq2
DESeq2
updated 11 months ago by
swbarnes2
★ 1.3k • written 11 months ago by
sara.p
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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