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Votes
0
votes
0
replies
6
views
Error "DESeqDataSetFromMatrix" function not found
GeneExpression
1 hour ago
Iraide
• 0
0
votes
1
reply
17
views
Can´t install GenomicRanges and rtracklayer
rtracklayer
GenomicRanges
Installation
updated 4 hours ago by
James W. MacDonald
60k • written 4 hours ago by
Johanna
• 0
0
votes
1
reply
41
views
How fix lines of dendrogram that overlap in the column portion of a heatmap?
heat
heatmaps
updated 11 hours ago by
James W. MacDonald
60k • written 1 day ago by
MauriAndres
• 0
0
votes
0
replies
13
views
set.seed in function vs clusterSetRNGStream: switching from one to another
parallel
seed
11 hours ago
ZheFrench
▴ 30
0
votes
0
replies
19
views
Compare different cell lines with tissues using limma
limma
MicroarrayData
Microarray
Agilent
12 hours ago
Sam
• 0
3
votes
2
replies
42
views
FeaturePlot in scater
scater
OSCA
15 hours ago • updated 10 hours ago
Guandong Shang
▴ 20
0
votes
1
reply
53
views
Analyzing barcode sequencing experiments with DESeq2/edgeR
edgeR
DESeq2
updated 22 hours ago by
Gordon Smyth
45k • written 1 day ago by
nc2849
• 0
0
votes
3
replies
64
views
How can i fix this problem in R
S4Vectors
DESeq2
updated 14 hours ago by
ATpoint
★ 1.3k • written 1 day ago by
Habib
• 0
0
votes
1
reply
35
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 1 day ago by
ATpoint
★ 1.3k • written 1 day ago by
otieno43
• 0
0
votes
0
replies
18
views
Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene
ChIPseeker
annotate
1 day ago
Palmira
• 0
0
votes
1
reply
32
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
updated 1 day ago by
Guido Hooiveld
★ 3.3k • written 1 day ago by
Bhavana
• 0
0
votes
1
reply
43
views
What are the data values in qRT-PCR for statistical testing? dCT? or 2^-dCT?
qRT-PCR
CTvalue
updated 1 day ago by
James W. MacDonald
60k • written 1 day ago by
Wendy
• 0
0
votes
1
reply
55
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq
DESeq2
updated 1 day ago by
ATpoint
★ 1.3k • written 1 day ago by
abdi.zhr26
• 0
9
votes
9
replies
208
views
Using Age or other numerical variable to model expression in deseq2
DESeq2
updated 11 hours ago by
James W. MacDonald
60k • written 2 days ago by
krushnach80
• 0
0
votes
0
replies
49
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
2 days ago
JAcky
• 0
0
votes
1
reply
62
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi
biomaRt
Bioconductor
updated 2 days ago by
Mike Smith
★ 5.6k • written 2 days ago by
sautik87_sit
• 0
0
votes
1
reply
55
views
Using queryMany() in mygene package: Problem of querying Entrez gene IDs based on UniGene IDs in rat.
mygene
queryMany
updated 2 days ago by
Guido Hooiveld
★ 3.3k • written 5 days ago by
chaof
• 0
0
votes
1
reply
67
views
GC content
EDASeq
updated 2 days ago by
ATpoint
★ 1.3k • written 5 days ago by
Matilde
• 0
0
votes
0
replies
29
views
Timeout error when querying DGIDB
rDGIdb
2 days ago
Jannah
• 0
0
votes
4
replies
124
views
I got error message about DESeqDataSetFromMatrix
DESeq2
updated 2 days ago by
swbarnes2
★ 1.1k • written 3 days ago by
Md. Faridul
• 0
2
votes
6
replies
480
views
DESeq2: relevel() unsuccessfully setting control group
DESeq2
updated 3 days ago by
Slot
• 0 • written 15 months ago by
vanbelj
▴ 10
1
vote
3
replies
234
views
miRNA differential expression analysis - treat as transcript level?
tximport
DESeq2
edgeR
swish
miRNA
updated 4 days ago by
Michael Love
37k • written 9 days ago by
BG
• 0
0
votes
0
replies
51
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow
DifferentialExpression
SingleCell
SingleCellMultiModal
MAST
5 days ago
Nik Tuzov
▴ 70
3
votes
9
replies
221
views
Help with limma contrast, difference of a difference?
limma
5 days ago
Ahdee
▴ 50
0
votes
6
replies
125
views
How to change all text, including point labels to Arial?
EnhancedVolcano
updated 5 days ago by
James W. MacDonald
60k • written 6 days ago by
junli1988
• 0
0
votes
0
replies
30
views
DiffBind: GreyListChIP error: Error: $ operator is invalid for atomic vectors
DiffBind
5 days ago
millerh1
• 0
0
votes
2
replies
76
views
Scaling for p.heatmap
heatmaps
pheatmap
scaling
5 days ago • updated 1 day ago
Bhavana
• 0
0
votes
4
replies
129
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
9 days ago • updated 2 days ago
Mohamed
• 0
0
votes
3
replies
91
views
I got error when visualizing my PCA
PCAtools
pcaExplorer
pcaMethods
updated 5 days ago by
Federico Marini
▴ 140 • written 5 days ago by
m610110001
• 0
0
votes
0
replies
42
views
Is there a Bioconductor package to calculate TFs regulatory networks?
TFs
Transcription
regulator
6 days ago
OliverBoynton
• 0
1
vote
3
replies
86
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation
GeneOntology
topGO
GO
updated 2 days ago by
James W. MacDonald
60k • written 6 days ago by
Raito92
▴ 60
1
vote
6
replies
138
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
6 days ago • updated 8 hours ago
Kelen
• 0
0
votes
0
replies
31
views
Typo in citation for RNASeqPower
RNASeqPower
citation
6 days ago
stephenjjohnson
• 0
0
votes
0
replies
29
views
diffbind dba.report
diffbind
6 days ago
jonathanho1989
• 0
0
votes
8
replies
224
views
Finding differentially expressed genes in a prospective cohort study
limma
MicroarrayData
Microarray
7 days ago • updated 2 days ago
YC
• 0
1
vote
4
replies
111
views
How to create an aldex.clr object from a "selex" data table
ALDEx2
7 days ago • updated 6 days ago
Greg
• 0
3
votes
5
replies
152
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 7 days ago by
shepherl
3.1k • written 8 days ago by
rama
▴ 10
0
votes
3
replies
108
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma
KEGGREST
EGSEA
updated 7 days ago by
shepherl
3.1k • written 8 days ago by
Jenny Drnevich
★ 2.0k
0
votes
1
reply
65
views
extendedSequences length is not the required for DeepCpf1 (34bp)
CRISPRseek
10 days ago • updated 7 days ago
Miguel
• 0
1
vote
2
replies
98
views
ENSEMBL to ENTREZ ID
clusterProfiler
7 days ago
martacrespi7
• 0
0
votes
2
replies
96
views
Error in NxtIRFcore
NxtIRFcore
IRFinder
7 days ago
ieki.tky
• 0
2
votes
3
replies
96
views
Large difference between lfcshrink and non-shrunk DESeq2 results
DESeq2
8 days ago • updated 7 days ago
Dave
• 0
0
votes
2
replies
87
views
Get confused about the mean log-intensity (Amean)
limma
8 days ago • updated 7 days ago
OE
• 0
1
vote
5
replies
118
views
Unable to load mm10 genome for use with GenomicDistributions package
GenomeInfoDb
GenomeInfoDbData
GenomicDistributionsData
GenomicDistributions
8 days ago • updated 7 days ago
rashford
• 0
0
votes
1
reply
72
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph
pathview
updated 8 days ago by
Guido Hooiveld
★ 3.3k • written 21 days ago by
k.jane.olczak
• 0
0
votes
0
replies
44
views
Diffbind analysis of ATAC-seq data
ATACSeq
DiffBind
8 days ago • updated 7 days ago
young
• 0
2
votes
2
replies
72
views
Can't load UCSC transcript IDs
RNASeq
updated 8 days ago by
Guido Hooiveld
★ 3.3k • written 8 days ago by
becker.jemima
• 0
3
votes
1
reply
112
views
RFC: Inconsistent software license for scran & automated license checks
agpl
license
gpl
scran
updated 8 days ago by
Vincent J. Carey, Jr.
6.6k • written 15 days ago by
matthias-doering
▴ 30
0
votes
20
replies
468
views
Different DESeq2 results (both FC and pvalue) by changing col/row orders in input
DESeq2
9 days ago • updated 7 days ago
Weisheng
• 0
1
vote
2
replies
107
views
deseq2 lfc shrinkage with few DEGs
RNASeq
DESeq2
9 days ago
Victor
• 0
42,718 results • Page
1 of 855
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Replies
Answer: Can´t install GenomicRanges and rtracklayer
by
James W. MacDonald
60k
You can't just call `BiocManager::install()` and expect it to know what you want to install! You need to specify the packages you want as a…
Comment: why org.Hs.egGO2ALLEGS contain genes number difference from GO database?
by
pengmin.wang.1
• 0
yes, I also find genes in org.Bt.egGO2ALLEGS (bovine) are always less than online GO database in the same term. So do you know how to get t…
Comment: how to get gene list for given GO terms?
by
pengmin.wang.1
• 0
Hi, do you know how to get the gene list that have annotations from online GO database. For example, y <- as.list(org.Bt.egGO2ALLEGS), y co…
Comment: RSEM - tximport; where is effective_length information used? Implications for sc
by
Kelen
• 0
Thank you. Gene-level analysis. I don't yet have a specific downstream pipeline in mind - I am trying to understand what limitations I migh…
Comment: FeaturePlot in scater
by
Guandong Shang
▴ 20
Thanks, this is what I want!
Votes
A: paired and unpaired test at the same time with voom limma
Comment: Duplicate correlation with limma in before-after exposure experiment
Answer: Using Age or other numerical variable to model expression in deseq2
Comment: Using Age or other numerical variable to model expression in deseq2
Comment: Using Age or other numerical variable to model expression in deseq2
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