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Views
Votes
0
votes
0
replies
8
views
Using Age or other numerical variable to model expression in deseq2
DESeq2
30 minutes ago
krushnach80
• 0
0
votes
1
reply
33
views
Using queryMany() in mygene package: Problem of querying Entrez gene IDs based on UniGene IDs in rat.
mygene
queryMany
updated 42 minutes ago by
Guido Hooiveld
★ 3.3k • written 2 days ago by
chaof
• 0
0
votes
1
reply
43
views
GC content
EDASeq
updated 52 minutes ago by
ATpoint
★ 1.3k • written 2 days ago by
Matilde
• 0
0
votes
0
replies
11
views
Timeout error when querying DGIDB
rDGIdb
5 hours ago
Jannah
• 0
0
votes
3
replies
64
views
I got error message about DESeqDataSetFromMatrix
DESeq2
23 hours ago • updated 7 hours ago
Md. Faridul
• 0
2
votes
6
replies
458
views
DESeq2: relevel() unsuccessfully setting control group
DESeq2
updated 21 hours ago by
Slot
• 0 • written 15 months ago by
vanbelj
▴ 10
1
vote
3
replies
195
views
miRNA differential expression analysis - treat as transcript level?
tximport
DESeq2
edgeR
swish
miRNA
updated 1 day ago by
Michael Love
37k • written 6 days ago by
BG
• 0
0
votes
0
replies
36
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow
DifferentialExpression
SingleCell
SingleCellMultiModal
MAST
2 days ago
Nik Tuzov
▴ 70
3
votes
9
replies
171
views
Help with limma contrast, difference of a difference?
limma
2 days ago
Ahdee
▴ 50
0
votes
6
replies
99
views
How to change all text, including point labels to Arial?
EnhancedVolcano
updated 2 days ago by
James W. MacDonald
60k • written 3 days ago by
junli1988
• 0
0
votes
0
replies
25
views
DiffBind: GreyListChIP error: Error: $ operator is invalid for atomic vectors
DiffBind
2 days ago
millerh1
• 0
0
votes
1
reply
47
views
Scaling for p.heatmap
heatmaps
pheatmap
scaling
updated 2 days ago by
Wolfgang Huber
13k • written 3 days ago by
Bhavana
• 0
0
votes
3
replies
89
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
updated 2 days ago by
ATpoint
★ 1.3k • written 6 days ago by
Mohamed
• 0
0
votes
3
replies
77
views
I got error when visualizing my PCA
PCAtools
pcaExplorer
pcaMethods
updated 2 days ago by
Federico Marini
▴ 140 • written 3 days ago by
m610110001
• 0
0
votes
0
replies
35
views
Is there a Bioconductor package to calculate TFs regulatory networks?
TFs
Transcription
regulator
3 days ago
OliverBoynton
• 0
0
votes
1
reply
52
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation
GeneOntology
topGO
GO
updated 3 days ago by
James W. MacDonald
60k • written 3 days ago by
Raito92
▴ 60
1
vote
2
replies
77
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
updated 2 days ago by
Michael Love
37k • written 3 days ago by
Kelen
• 0
0
votes
0
replies
26
views
Typo in citation for RNASeqPower
RNASeqPower
citation
3 days ago
stephenjjohnson
• 0
0
votes
0
replies
23
views
diffbind dba.report
diffbind
3 days ago
jonathanho1989
• 0
0
votes
8
replies
188
views
Finding differentially expressed genes in a prospective cohort study
limma
MicroarrayData
Microarray
5 days ago • updated 4 hours ago
YC
• 0
1
vote
4
replies
94
views
How to create an aldex.clr object from a "selex" data table
ALDEx2
4 days ago • updated 3 days ago
Greg
• 0
3
votes
5
replies
124
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 4 days ago by
shepherl
3.1k • written 5 days ago by
rama
▴ 10
0
votes
3
replies
94
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma
KEGGREST
EGSEA
updated 4 days ago by
shepherl
3.1k • written 5 days ago by
Jenny Drnevich
★ 2.0k
0
votes
1
reply
60
views
extendedSequences length is not the required for DeepCpf1 (34bp)
CRISPRseek
7 days ago • updated 4 days ago
Miguel
• 0
1
vote
2
replies
88
views
ENSEMBL to ENTREZ ID
clusterProfiler
4 days ago
martacrespi7
• 0
0
votes
2
replies
89
views
Error in NxtIRFcore
NxtIRFcore
IRFinder
5 days ago • updated 4 days ago
ieki.tky
• 0
2
votes
3
replies
86
views
Large difference between lfcshrink and non-shrunk DESeq2 results
DESeq2
5 days ago • updated 4 days ago
Dave
• 0
0
votes
2
replies
76
views
Get confused about the mean log-intensity (Amean)
limma
5 days ago • updated 4 days ago
OE
• 0
1
vote
5
replies
105
views
Unable to load mm10 genome for use with GenomicDistributions package
GenomeInfoDb
GenomeInfoDbData
GenomicDistributionsData
GenomicDistributions
5 days ago • updated 4 days ago
rashford
• 0
0
votes
1
reply
66
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph
pathview
updated 5 days ago by
Guido Hooiveld
★ 3.3k • written 18 days ago by
k.jane.olczak
• 0
0
votes
0
replies
40
views
Diffbind analysis of ATAC-seq data
ATACSeq
DiffBind
5 days ago • updated 4 days ago
young
• 0
2
votes
2
replies
62
views
Can't load UCSC transcript IDs
RNASeq
updated 5 days ago by
Guido Hooiveld
★ 3.3k • written 5 days ago by
becker.jemima
• 0
3
votes
1
reply
105
views
RFC: Inconsistent software license for scran & automated license checks
agpl
license
gpl
scran
updated 6 days ago by
Vincent J. Carey, Jr.
6.6k • written 12 days ago by
matthias-doering
▴ 30
0
votes
20
replies
433
views
Different DESeq2 results (both FC and pvalue) by changing col/row orders in input
DESeq2
6 days ago • updated 4 days ago
Weisheng
• 0
1
vote
2
replies
100
views
deseq2 lfc shrinkage with few DEGs
RNASeq
DESeq2
6 days ago
Victor
• 0
0
votes
3
replies
106
views
Persisting error in making a heatmap
heatmaps
gplots
7 days ago • updated 4 days ago
beslinail
• 0
3
votes
3
replies
131
views
Nested analysis or Collapsed-replicate analysis?
RNASeq
DESeq2
updated 6 days ago by
Michael Love
37k • written 16 days ago by
giulia.lopatriello
• 0
0
votes
0
replies
49
views
BiocParallel error with ChIPQC
BiocManager
ChIPQC
RSamtools
BiocParallel
7 days ago • updated 6 days ago
etiennedanis
• 0
3
votes
9
replies
267
views
How many features an ExpressionSet can contain ?
ExpressionSet
9 days ago • updated 4 days ago
OE
• 0
0
votes
1
reply
86
views
Interpretation of comparison results in nested designs
DESeq2
updated 7 days ago by
Michael Love
37k • written 9 days ago by
thkapell
▴ 10
0
votes
0
replies
39
views
stuck on unimplemented type 'list' in 'EncodeElement'
list
save
dataframe
updated 5 days ago by
shepherl
3.1k • written 7 days ago by
orticello.1160797
• 0
0
votes
2
replies
87
views
I need cancer databases suggestion
#ccle
#tcga
#cancer
updated 5 days ago by
Marcel Ramos
570 • written 8 days ago by
UGUR
• 0
0
votes
6
replies
204
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
updated 5 days ago by
Aaron Lun
★ 27k • written 10 days ago by
pcantalupo
• 0
2
votes
9
replies
231
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA
r
RNASeqData
voom
limma
9 days ago • updated 3 days ago
Peipei
• 0
0
votes
1
reply
42
views
Check the CummeRbund PDF.
cummeRbund
updated 5 days ago by
shepherl
3.1k • written 9 days ago by
peter.r.hoyt
• 0
1
vote
5
replies
125
views
Can't read in CEL files
GEO
GEOquery
10 days ago
OE
• 0
0
votes
0
replies
40
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
10 days ago • updated 9 days ago
xubeisi
• 0
1
vote
3
replies
270
views
Error in shrinkage for DESeq2
sva
DESeq2
11 days ago
Kent
• 0
3
votes
3
replies
98
views
ComplexHeatmap install error
ComplexHeatmap
updated 11 days ago by
James W. MacDonald
60k • written 11 days ago by
nalaspina
• 0
1
vote
3
replies
188
views
Obtaining many more significant differentially expressed genes by subsetting than just using contrasts
DESeq2
updated 10 days ago by
Michael Love
37k • written 12 days ago by
Tom
▴ 10
42,703 results • Page
1 of 855
Recent ...
Replies
Answer: Using queryMany() in mygene package: Problem of querying Entrez gene IDs based o
by
Guido Hooiveld
★ 3.3k
I am not familiar with the package `mygene`, but please note that unigene has been retired 3 years ago! https://ncbiinsights.ncbi.nlm.nih.g…
Comment: GC content
by
ATpoint
★ 1.3k
To be all honest with you, work for example by Mike Love has shown that accurately modeling the GC content for expression data relies on ac…
Answer: GC content
by
Robert Castelo
★ 2.9k
hi, The help page of `getGeneLengthAndGCContent()` says that this function "Automatically retrieves gene length and GC-content informati…
Comment: Finding differentially expressed genes in a prospective cohort study
by
YC
• 0
Thank you for your explanation and clarification. So, if I understand right, the purpose of building linear models in LIMMA is to find diff…
Comment: I got error message about DESeqDataSetFromMatrix
by
Md. Faridul
• 0
I run the library(DESeq2) then got error message. I am new in r. How to solve this error. Error: package or namespace load failed for ‘DES…
Votes
C: Converting numeric variables to factors in DESeq metadata
C: Converting numeric variables to factors in DESeq metadata
Comment: miRNA differential expression analysis - treat as transcript level?
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
Comment: RSEM - tximport; where is effective_length information used? Implications for sc
Awards
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to
Michael Love
37k
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to
Gordon Smyth
45k
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to
James W. MacDonald
60k
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to
Nik Tuzov
▴ 70
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to
Kevin Blighe
3.5k
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