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Filtering
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0
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2
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685
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Mean variance curve troubleshoot filtering
limmavoom
filtering
edgeR
RNASeqData
meanvariancetrend
10 months ago
gingergeiger22
• 0
0
votes
1
reply
820
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering
DESeq2
outliers
updated 15 months ago by
Michael Love
43k • written 15 months ago by
smac_head
• 0
3
votes
11
replies
2.3k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering
STD
DEG
limma
updated 2.4 years ago by
Gordon Smyth
53k • written 2.4 years ago by
alexia.brunel
• 0
5
votes
7
replies
2.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
mohammedtoufiq91
▴ 10
5
votes
8
replies
3.0k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression
R
filtering
limma
3.1 years ago • updated 2.9 years ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
813
views
Filtering single-channel Affymetrix probes
filtering
probe
MicroarrayData
3.2 years ago
Fatemeh
• 0
3
votes
5
replies
3.0k
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 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
svlachavas
▴ 840
0
votes
0
replies
1.5k
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks
filtering
gdc
TCGABiolinks
rnaseq
5.8 years ago
jam526
• 0
2
votes
4
replies
2.9k
views
Filtering, minimum sample number, and condition in edgeR
edger
filtering
updated 6.9 years ago by
Ryan C. Thompson
★ 7.9k • written 6.9 years ago by
rproendo
▴ 30
0
votes
1
reply
1.4k
views
How to keep the genes whose counts are equal or greater than 10
deseq2
filtering
updated 7.0 years ago by
James W. MacDonald
68k • written 7.0 years ago by
n_h_78
• 0
1
vote
1
reply
1.3k
views
DeSeq2 independant filtering barely removes any genes
deseq2
differential gene expression
filtering
updated 7.3 years ago by
Michael Love
43k • written 7.4 years ago by
mnaymik
• 0
1
vote
2
replies
1.6k
views
Filtering Rna-seq counts
rna-seq
filtering
updated 7.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
Aurora
▴ 20
5
votes
12
replies
9.4k
views
Filtering step for differential analysis in edgeR
r
edger
differential gene expression
filtering
bioconductor
updated 7.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
Biologist
▴ 120
4
votes
8
replies
2.2k
views
edgeR error when trying to filter peaks with low read counts
edger
R
filtering
7.6 years ago
camerond
• 0
0
votes
2
replies
1.7k
views
Filtering genes with a minimum number of counts between samples
DESeq2
filtering
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
A
▴ 60
1
vote
1
reply
2.4k
views
Filtering a BED file according to genomic annotation
bed files
bedtools
filtering
chipseq
updated 7.8 years ago by
Aaron Lun
★ 29k • written 7.8 years ago by
rbronste
▴ 60
0
votes
2
replies
2.2k
views
DiffBind remove low count intervals for differential analysis
diffbind
filtering
7.9 years ago
gasta88
• 0
0
votes
2
replies
1.5k
views
DiffBind dba.report inconsistent output when using filter parameters
diffbind
dba.report
filtering
8.0 years ago
konstantopoulos
• 0
1
vote
3
replies
6.3k
views
DESeq2: How to manually perform filtering and outlier detection?
deseq2
filtering
outliers
count outliers
updated 8.2 years ago by
Wolfgang Huber
★ 13k • written 8.2 years ago by
heikki.sarin
▴ 10
1
vote
6
replies
2.5k
views
Nonspecific filtering of microarray data
microarray
affymetrix microarrays
pre-filtering
filtering
nonspecific filtering
updated 8.4 years ago by
Wolfgang Huber
★ 13k • written 8.4 years ago by
n.lu
• 0
2
votes
2
replies
1.4k
views
Limma filtering based on treatment group
limma
filtering
updated 8.5 years ago by
Steve Lianoglou
★ 13k • written 8.5 years ago by
jamie.gearing
▴ 60
3
votes
4
replies
1.8k
views
Any way to detach or simplify nested GRangesList ?
grangeslist
filtering
r
9.1 years ago
Jurat Shahidin
▴ 80
1
vote
2
replies
2.5k
views
edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
edger
filtering
cpm
updated 9.2 years ago by
Gordon Smyth
53k • written 9.2 years ago by
lynski008
• 0
6
votes
4
replies
2.3k
views
Filtering after a contrast
deseq2
r
filtering
bioconductor
updated 9.2 years ago by
Steve Lianoglou
★ 13k • written 9.2 years ago by
rattigak
• 0
0
votes
1
reply
1.4k
views
Does the normalization pipeline for scran include filtering out genes with low counts?
filtering
scran
updated 9.2 years ago by
Aaron Lun
★ 29k • written 9.2 years ago by
amckenz
• 0
9
votes
12
replies
11k
views
Filtering of RNA-seq data in EdgeR
rnaseq
edger
filtering
written 9.5 years ago by
alireza_sharifian_10
▴ 20
5
votes
12
replies
2.9k
views
Filtering before the linear modelling and empirical bayes steps
DEG
Limma
Filtering
updated 9.6 years ago by
Ryan C. Thompson
★ 7.9k • written 9.6 years ago by
Shamim Sarhadi
▴ 20
2
votes
4
replies
2.7k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
affymetrix
limma
filtering
updated 10.5 years ago by
James W. MacDonald
68k • written 10.5 years ago by
ablanchetcohen
• 0
2
votes
7
replies
3.2k
views
Different filters with edgeR
edger
filtering
10.6 years ago
cpcantalapiedra
• 0
3
votes
10
replies
3.1k
views
Question about converting rownames of an expression dataset to their corresponding gene symbols
filtering
bioconductor
genesymbols
expressionset
10.6 years ago
svlachavas
▴ 840
30 results • Page
1 of 1
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Comment: VariantAnnotation does escape = within header string quotes
by
Daniel Cameron
▴ 40
I'm just stripping the entire line as a workaround using `meta(header(vcf))$DRAGENCommandLine = NULL`. Not ideal but at least subsequent pa…
Comment: Setting up a DESeq2 Design with Paired Data
by
Alexander
• 0
Hi Kevin, Firstly, thank you so much for not only a very prompt response, but one that is incredibly insightful and helps me learn DESeq2 …
Comment: featureCounts -L: high unassigned:mapq fraction
by
eja.gssssssse.r.m
• 0
If you re looking to enjoy a fun mobile experience, the 3 patti vegas game offers a seamless way to play classic card games on your phone. …
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
by
Kevin Blighe
★ 4.0k
Hello Matthew, Thanks for the detailed description-this sounds like a classic challenge in sncRNA analysis, where piRNAs (and other tsRN…
Answer: VariantAnnotation does escape = within header string quotes
by
Kevin Blighe
★ 4.0k
Hi, Thanks for the minimal reproduction - this is very clear and confirms a bug in `VariantAnnotation::writeVcf()`. The issue is that th…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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shepherl
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James W. MacDonald
68k
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Daniel Cameron
▴ 40
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Peter Hickey
▴ 760
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