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0
votes
0
replies
8
views
rename phenotypic variables in pData (microarray) or colData (RNA-Seq)
PhenoGeneRanker
3 hours ago
jogugil
• 0
0
votes
1
reply
27
views
Error
DESeq2
updated 8 hours ago by
ATpoint
★ 1.3k • written 12 hours ago by
Mahsa
• 0
0
votes
0
replies
27
views
Can't Install ensembldb and EnsDb.Hsapiens.v86
installation
EnsDb.Hsapiens.v86
Bioconductor
package
ensembldb
18 hours ago
elmfinds
• 0
1
vote
3
replies
73
views
How to get DESeq2 results for a list of genes
DESeq2
updated 3 hours ago by
ATpoint
★ 1.3k • written 1 day ago by
Lucía
▴ 10
0
votes
0
replies
37
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
1 day ago
Simon Coetzee
▴ 50
1
vote
1
reply
44
views
ComplexHeatmap: Change font size of annotation axis values
ComplexHeatmap
1 day ago
nalaspina
• 0
1
vote
1
reply
37
views
setting sizeFactors from scran :: caculateSumFactors.
scran
DESeq2
updated 1 day ago by
ATpoint
★ 1.3k • written 2 days ago by
OE
• 0
0
votes
4
replies
856
views
Suggesting changing the "reply-to" field to the mailing list address.
updated 2 days ago by
gracyjones60
• 0 • written 12.9 years ago by
Peng Yu
▴ 940
3
votes
12
replies
526
views
cellCounts() function floating point error
Rsubread
updated 2 days ago by
Yang Liao
▴ 340 • written 8 weeks ago by
J-E
• 0
0
votes
2
replies
60
views
Unable to open hd5 file using rhdf5 but can list contents
hdf5
h5
rhdf5
updated 2 days ago by
Mike Smith
★ 5.6k • written 3 days ago by
dNand
• 0
0
votes
2
replies
81
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges
plyranges
2 days ago
Rodrigo
• 0
4
votes
5
replies
98
views
package 'BiocInstaller' is not available (for R version 3.4.4)
BiocInstaller
updated 2 days ago by
James W. MacDonald
60k • written 2 days ago by
Kevin
• 0
2
votes
6
replies
110
views
Limma beta coefficient confidence intervals
limma
limmaGUI
beta
2 days ago
fluentin44
• 0
0
votes
4
replies
98
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 2 days ago by
Gordon Smyth
45k • written 3 days ago by
Mohamed
• 0
0
votes
4
replies
73
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
3 days ago • updated 2 days ago
uhlkatie
• 0
0
votes
1
reply
46
views
how to get the gene set from online GO database
clusterProfiler
WebGestalR
updated 3 days ago by
James W. MacDonald
60k • written 3 days ago by
pengmin.wang.1
• 0
0
votes
0
replies
22
views
coseq does not find object "cap"
coseq
3 days ago
JaneDoe
• 0
0
votes
0
replies
30
views
Pick some clusters to run trajectory and pseudotime analysis on Monocle3
SpecificClusters
TrajectoryAnalysis
PseudotimeAnalysis
Monocle3
3 days ago
martacrespi7
• 0
0
votes
0
replies
24
views
Calculating tumour purity having only CNA data
PureCN
CNA
purity
cancer
3 days ago
JAcky
• 0
0
votes
2
replies
57
views
bootstrapNullAlternativeModel() returns error
TPP2D
3 days ago
Tobias
▴ 30
0
votes
0
replies
41
views
During dba(sampleSheet = "samples.csv") step, Error in mergeScores(merged, def, peakset, TRUE) : Not compatible with requested type: [type=charac…
DiffBind
3 days ago
niimabear
• 0
0
votes
1
reply
54
views
Compare different cell lines with tissues using limma
limma
MicroarrayData
Microarray
Agilent
updated 3 days ago by
Gordon Smyth
45k • written 4 days ago by
Sam
• 0
0
votes
1
reply
44
views
Error "DESeqDataSetFromMatrix" function not found
GeneExpression
updated 3 days ago by
Basti
▴ 330 • written 3 days ago by
Iraide
• 0
0
votes
1
reply
47
views
Can´t install GenomicRanges and rtracklayer
rtracklayer
GenomicRanges
Installation
updated 3 days ago by
James W. MacDonald
60k • written 3 days ago by
Johanna
• 0
0
votes
1
reply
58
views
How fix lines of dendrogram that overlap in the column portion of a heatmap?
heat
heatmaps
updated 4 days ago by
James W. MacDonald
60k • written 4 days ago by
MauriAndres
• 0
0
votes
0
replies
26
views
set.seed in function vs clusterSetRNGStream: switching from one to another
parallel
seed
4 days ago
ZheFrench
▴ 30
3
votes
2
replies
70
views
FeaturePlot in scater
scater
OSCA
4 days ago
Guandong Shang
▴ 20
0
votes
1
reply
83
views
Analyzing barcode sequencing experiments with DESeq2/edgeR
edgeR
DESeq2
updated 4 days ago by
Gordon Smyth
45k • written 4 days ago by
nc2849
• 0
0
votes
3
replies
107
views
How can i fix this problem in R
S4Vectors
DESeq2
updated 4 days ago by
ATpoint
★ 1.3k • written 4 days ago by
Habib
• 0
0
votes
1
reply
54
views
Use of Scater for QC in scRNA-seq: How to remove cells with less than certain number of genes supported with certain number of reads
SingleCellExperiment
updated 4 days ago by
ATpoint
★ 1.3k • written 4 days ago by
otieno43
• 0
0
votes
0
replies
30
views
Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene
ChIPseeker
annotate
4 days ago
Palmira
• 0
0
votes
2
replies
73
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
4 days ago • updated 3 days ago
Bhavana
• 0
0
votes
1
reply
60
views
What are the data values in qRT-PCR for statistical testing? dCT? or 2^-dCT?
qRT-PCR
CTvalue
updated 4 days ago by
James W. MacDonald
60k • written 5 days ago by
Wendy
• 0
0
votes
1
reply
68
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq
DESeq2
updated 5 days ago by
ATpoint
★ 1.3k • written 5 days ago by
abdi.zhr26
• 0
9
votes
9
replies
276
views
Using Age or other numerical variable to model expression in deseq2
DESeq2
updated 4 days ago by
James W. MacDonald
60k • written 6 days ago by
krushnach80
• 0
0
votes
0
replies
67
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
6 days ago
JAcky
• 0
0
votes
1
reply
74
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi
biomaRt
Bioconductor
updated 6 days ago by
Mike Smith
★ 5.6k • written 6 days ago by
sautik87_sit
• 0
0
votes
1
reply
70
views
Using queryMany() in mygene package: Problem of querying Entrez gene IDs based on UniGene IDs in rat.
mygene
queryMany
updated 6 days ago by
Guido Hooiveld
★ 3.3k • written 8 days ago by
chaof
• 0
0
votes
1
reply
81
views
GC content
EDASeq
updated 6 days ago by
ATpoint
★ 1.3k • written 8 days ago by
Matilde
• 0
0
votes
0
replies
36
views
Timeout error when querying DGIDB
rDGIdb
6 days ago
Jannah
• 0
0
votes
4
replies
150
views
I got error message about DESeqDataSetFromMatrix
DESeq2
updated 6 days ago by
swbarnes2
★ 1.1k • written 7 days ago by
Md. Faridul
• 0
2
votes
6
replies
493
views
DESeq2: relevel() unsuccessfully setting control group
DESeq2
updated 7 days ago by
Slot
• 0 • written 15 months ago by
vanbelj
▴ 10
1
vote
3
replies
252
views
miRNA differential expression analysis - treat as transcript level?
tximport
DESeq2
edgeR
swish
miRNA
updated 7 days ago by
Michael Love
37k • written 13 days ago by
BG
• 0
0
votes
0
replies
56
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow
DifferentialExpression
SingleCell
SingleCellMultiModal
MAST
8 days ago
Nik Tuzov
▴ 70
3
votes
9
replies
238
views
Help with limma contrast, difference of a difference?
limma
8 days ago
Ahdee
▴ 50
0
votes
6
replies
133
views
How to change all text, including point labels to Arial?
EnhancedVolcano
updated 8 days ago by
James W. MacDonald
60k • written 9 days ago by
junli1988
• 0
0
votes
0
replies
35
views
DiffBind: GreyListChIP error: Error: $ operator is invalid for atomic vectors
DiffBind
9 days ago
millerh1
• 0
0
votes
2
replies
92
views
Scaling for p.heatmap
heatmaps
pheatmap
scaling
9 days ago • updated 5 days ago
Bhavana
• 0
0
votes
4
replies
145
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
12 days ago • updated 6 days ago
Mohamed
• 0
0
votes
3
replies
102
views
I got error when visualizing my PCA
PCAtools
pcaExplorer
pcaMethods
updated 8 days ago by
Federico Marini
▴ 140 • written 9 days ago by
m610110001
• 0
42,737 results • Page
1 of 855
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Replies
Comment: How to get DESeq2 results for a list of genes
by
ATpoint
★ 1.3k
That's a problem related to your lack of R basics, neither DESeq2 or Bioconductor software/technical problem. Please learn R basics first. …
Comment: How to get DESeq2 results for a list of genes
by
Lucía
▴ 10
Hi, thank you! Unfortunately that doesn't work. The first option gives me this error: ``` # Extracting for list my_genes <- read.delim("di…
Comment: Error
by
ATpoint
★ 1.3k
https://github.com/conda-forge/rpy2-feedstock/issues/1
Comment: Error: BiocParallel errors
by
lxl13260684135
• 0
I came across the same problem, have you solved it?
Answer: How to get DESeq2 results for a list of genes
by
ATpoint
★ 1.3k
Standard rules apply for filtering in R. If the genes are the rownames of the results object `res` then: res[my_ges,] or if the colu…
Votes
C: DESEQ2 'results' filter by value for multiple conditions (contrast off?)
C: DESEQ2 'results' filter by value for multiple conditions (contrast off?)
How to get DESeq2 results for a list of genes
Answer: setting sizeFactors from scran :: caculateSumFactors.
Answer: ComplexHeatmap: Change font size of annotation axis values
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