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Showing :
filtering
•
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0
votes
2
replies
258
views
Mean variance curve troubleshoot filtering
limmavoom
filtering
edgeR
RNASeqData
meanvariancetrend
25 days ago • updated 23 days ago
gingergeiger22
• 0
0
votes
1
reply
589
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering
DESeq2
outliers
updated 6 months ago by
Michael Love
43k • written 6 months ago by
smac_head
• 0
3
votes
11
replies
1.8k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering
STD
DEG
limma
updated 19 months ago by
Gordon Smyth
52k • written 19 months ago by
alexia.brunel
• 0
5
votes
7
replies
1.7k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 20 months ago by
Gordon Smyth
52k • written 20 months ago by
mohammedtoufiq91
▴ 10
5
votes
8
replies
2.5k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression
R
filtering
limma
2.4 years ago • updated 2.2 years ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
682
views
Filtering single-channel Affymetrix probes
filtering
probe
MicroarrayData
2.5 years ago
Fatemeh
• 0
3
votes
5
replies
2.6k
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq
rna-seq
filtering
DE
deseq2
updated 4.8 years ago by
Michael Love
43k • written 4.8 years ago by
svlachavas
▴ 840
0
votes
0
replies
1.3k
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks
filtering
gdc
TCGABiolinks
rnaseq
5.0 years ago
jam526
• 0
2
votes
4
replies
2.3k
views
Filtering, minimum sample number, and condition in edgeR
edger
filtering
updated 6.2 years ago by
Ryan C. Thompson
★ 7.9k • written 6.2 years ago by
rproendo
▴ 30
0
votes
1
reply
1.1k
views
How to keep the genes whose counts are equal or greater than 10
deseq2
filtering
updated 6.2 years ago by
James W. MacDonald
67k • written 6.2 years ago by
n_h_78
• 0
1
vote
1
reply
1.0k
views
DeSeq2 independant filtering barely removes any genes
deseq2
differential gene expression
filtering
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
mnaymik
• 0
1
vote
2
replies
1.3k
views
Filtering Rna-seq counts
rna-seq
filtering
updated 6.7 years ago by
Gordon Smyth
52k • written 6.7 years ago by
Aurora
▴ 20
5
votes
12
replies
7.9k
views
Filtering step for differential analysis in edgeR
r
edger
differential gene expression
filtering
bioconductor
updated 6.7 years ago by
Gordon Smyth
52k • written 6.7 years ago by
Biologist
▴ 120
4
votes
8
replies
1.8k
views
edgeR error when trying to filter peaks with low read counts
edger
R
filtering
6.8 years ago
camerond
• 0
0
votes
2
replies
1.4k
views
Filtering genes with a minimum number of counts between samples
DESeq2
filtering
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
A
▴ 40
1
vote
1
reply
2.0k
views
Filtering a BED file according to genomic annotation
bed files
bedtools
filtering
chipseq
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
rbronste
▴ 60
0
votes
2
replies
2.0k
views
DiffBind remove low count intervals for differential analysis
diffbind
filtering
7.2 years ago • updated 7.1 years ago
gasta88
• 0
0
votes
2
replies
1.3k
views
DiffBind dba.report inconsistent output when using filter parameters
diffbind
dba.report
filtering
7.2 years ago
konstantopoulos
• 0
1
vote
3
replies
5.8k
views
DESeq2: How to manually perform filtering and outlier detection?
deseq2
filtering
outliers
count outliers
updated 7.5 years ago by
Wolfgang Huber
★ 13k • written 7.5 years ago by
heikki.sarin
▴ 10
1
vote
6
replies
2.2k
views
Nonspecific filtering of microarray data
microarray
affymetrix microarrays
pre-filtering
filtering
nonspecific filtering
updated 7.7 years ago by
Wolfgang Huber
★ 13k • written 7.7 years ago by
n.lu
• 0
2
votes
2
replies
1.2k
views
Limma filtering based on treatment group
limma
filtering
updated 7.7 years ago by
Steve Lianoglou
★ 13k • written 7.7 years ago by
jamie.gearing
▴ 60
3
votes
4
replies
1.5k
views
Any way to detach or simplify nested GRangesList ?
grangeslist
filtering
r
8.4 years ago • updated 8.3 years ago
Jurat Shahidin
▴ 80
1
vote
2
replies
2.3k
views
edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
edger
filtering
cpm
updated 8.4 years ago by
Gordon Smyth
52k • written 8.4 years ago by
lynski008
• 0
6
votes
4
replies
2.0k
views
Filtering after a contrast
deseq2
r
filtering
bioconductor
updated 8.5 years ago by
Steve Lianoglou
★ 13k • written 8.5 years ago by
rattigak
• 0
0
votes
1
reply
1.2k
views
Does the normalization pipeline for scran include filtering out genes with low counts?
filtering
scran
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
amckenz
• 0
9
votes
11
replies
10k
views
Filtering of RNA-seq data in EdgeR
rnaseq
edger
filtering
updated 8.6 years ago by
David ROUX
▴ 20 • written 8.7 years ago by
alireza_sharifian_10
▴ 20
5
votes
12
replies
2.3k
views
Filtering before the linear modelling and empirical bayes steps
DEG
Limma
Filtering
updated 8.8 years ago by
Ryan C. Thompson
★ 7.9k • written 8.9 years ago by
Shamim Sarhadi
▴ 20
2
votes
4
replies
2.4k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
affymetrix
limma
filtering
updated 9.7 years ago by
James W. MacDonald
67k • written 9.7 years ago by
ablanchetcohen
• 0
2
votes
7
replies
3.0k
views
Different filters with edgeR
edger
filtering
9.8 years ago
cpcantalapiedra
• 0
3
votes
10
replies
2.7k
views
Question about converting rownames of an expression dataset to their corresponding gene symbols
filtering
bioconductor
genesymbols
expressionset
9.9 years ago
svlachavas
▴ 840
30 results • Page
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kl2023gege
• 0
Thanks for sharing. You gotta check out Sprunki Phase Games on [Sprunki Phase](https://sprunkiphase.net). It's a wild ride of tunes and tw…
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
Quang NN
▴ 10
I see. Thank you ATpoint!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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