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Gene
•
reset
0
votes
5
replies
6.2k
views
Adding information to the DESeq2 output file (gene name and expression levels for each sample(
deseq2
gene
columns
output
updated 8.5 years ago by
Michael Love
41k • written 8.5 years ago by
amyfm
▴ 10
0
votes
2
replies
3.7k
views
Gene body coverage plot
plot
gene
GenomicRanges
Coverage
R
updated 2.1 years ago by
kent.riemondy
▴ 20 • written 2.1 years ago by
svenbioinf
• 0
0
votes
2
replies
3.6k
views
Web Scraping From Pubmd (I want to extract gene articles form pubmed abstract and pubmed id i want to extract for number of genes)
cancer
gene
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
venkatarao142152
• 0
3
votes
2
replies
3.5k
views
How to Find OMIM id's Corresponding to a List of Gene Symbols in R?
microarray
omim
gene
disorder
updated 9.1 years ago by
Kamil Slowikowski
▴ 30 • written 9.1 years ago by
pankajnarula84
▴ 20
6
votes
2
replies
2.2k
views
How to add my own Entrez Gene IDs rather than using the ones from a default package?
annotation
entrez
gene
ids
software error
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
Raito92
▴ 60
6
votes
7
replies
2.2k
views
GEOquery reading error on Windows.
GEOquery
GEO
Gene
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
Caitlin
▴ 50
5
votes
5
replies
1.9k
views
threeUTRsByTranscript per GENE
GenomicFeatures
Transcript
gene
threeUTRsByTranscript
updated 3.2 years ago by
Dario Strbenac
★ 1.5k • written 4.7 years ago by
amgtech
▴ 10
1
vote
3
replies
1.7k
views
copy number variation analysis (CNV)
copynumber
plot
visualization
NGS
gene
updated 3.4 years ago by
Ram
▴ 190 • written 3.5 years ago by
sijing.gsj
• 0
0
votes
2
replies
1.6k
views
How to filter the coding protein genes by EnsDb.Hsapiens.v86
EnsDb.Hsapiens.v86
gene
2.1 years ago
beslinail
• 0
9
votes
10
replies
1.4k
views
Mapping of GENE symbols into ENTREZ
limma
annotation
Gene
4.6 years ago • updated 4.2 years ago
omarrafiqued
▴ 50
2
votes
5
replies
1.2k
views
DESeq2-result files (.csv): Is there a convention for the IDs (e.g. gene names if produced for genes)
deseq2
gene
format
4.8 years ago
miriam.mueller
• 0
3
votes
3
replies
1.2k
views
Discrepancies between topGO output and input
go
topGO
gene
ontology
enrichment
updated 4.8 years ago by
James W. MacDonald
65k • written 4.8 years ago by
t.bergmann
• 0
1
vote
4
replies
1.1k
views
gene Isoforms quantification using RNA-seq data
gene
isoform
quantification
rna-seq
updated 4.7 years ago by
swbarnes2
★ 1.3k • written 4.7 years ago by
angel.campos
• 0
0
votes
3
replies
1.0k
views
PureCN gene LOH very common, amp/del not
PureCN
gene
amplification
deletion
loh
updated 4.0 years ago by
markus.riester
▴ 130 • written 4.0 years ago by
twtoal
▴ 10
0
votes
2
replies
1.0k
views
I want to use global test.
gene
r
clst
rpy
globaltest
3.1 years ago
Kim
• 0
0
votes
4
replies
992
views
Fonction of genes/metabolites in a pathway?
gene
metabolite
functionnal annotation
pathways
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
emisecherre
• 0
2
votes
4
replies
958
views
Joint pathway Analysis using both gene and metabolite data sets
data integration
gene
metabolite
4.1 years ago
emisecherre
• 0
0
votes
1
reply
807
views
WGCNA - Network construction and module detection
gene
Clustering
wgcna
flashclust
updated 20 months ago by
andres.firrincieli
▴ 50 • written 20 months ago by
Recep
▴ 20
1
vote
4
replies
795
views
RNA-seq analysis between a wildtype vs a double microRNA kockout mouse brain
microRNA
gene
RNASeqRData
edgeR
geneontology
18 months ago
faiza
• 0
1
vote
2
replies
724
views
gene ontologies for a set of genes
gene
ontology
2.7 years ago
Bogdan
▴ 670
0
votes
0
replies
625
views
TFutils database
TFutils
mouse
gene
convert
2.9 years ago
nicocillari
• 0
0
votes
2
replies
544
views
How to find the number of protein-coding genes in each chromosome arm in human?
gene
chromosome
proteincodinggene
12 months ago
Liliian
• 0
3
votes
2
replies
534
views
please resolve the issue
gene
ExpressionData
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
sonal
• 0
0
votes
0
replies
526
views
Gene expression changes in one condition
RNASeq
Gene
ExpressionData
2.5 years ago
AZ
▴ 30
0
votes
0
replies
451
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene
enrichment
topGO
GO
retrieve
12 months ago
Priya
• 0
0
votes
1
reply
291
views
gene aligning reference
geneRecommender
gene
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
Gülsüm
• 0
26 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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50k
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