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3
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Error in msaFun Cannot open input file. No alignment!
msa
21 minutes ago
Kamil Slowikowski
▴ 30
0
votes
1
reply
46
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 49 minutes ago by
Gordon Smyth
50k • written 11 hours ago by
JKim
• 0
0
votes
0
replies
13
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
2 hours ago
Julie
• 0
0
votes
0
replies
11
views
Help with Complex DESeq2 Design
DESeq2
3 hours ago
kelsey.beavers
• 0
3
votes
1
reply
44
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
updated 3 hours ago by
James W. MacDonald
65k • written 9 hours ago by
Georg
• 0
1
vote
0
replies
30
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
8 hours ago
andrebolerbarros
▴ 30
3
votes
15
replies
2.5k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
8 months ago • updated 11 hours ago
shepherl
3.8k
1
vote
2
replies
98
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
13 hours ago • updated 8 hours ago
Eva
▴ 10
0
votes
1
reply
56
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
updated 12 hours ago by
James W. MacDonald
65k • written 16 hours ago by
Efra
• 0
0
votes
1
reply
45
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 14 hours ago by
Michael Love
41k • written 1 day ago by
Emma
• 0
0
votes
1
reply
33
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 14 hours ago by
Michael Love
41k • written 15 hours ago by
rahaf.nazzal9
• 0
0
votes
1
reply
40
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Yuqin
• 0
1
vote
7
replies
1.0k
views
enrichGOgradient color change
clusterProfiler
updated 1 day ago by
Guido Hooiveld
★ 3.9k • written 4 months ago by
inna.gur
• 0
1
vote
5
replies
257
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
10 days ago • updated 1 day ago
Gerhard Thallinger
▴ 180
0
votes
1
reply
76
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 21 hours ago by
Gordon Smyth
50k • written 2 days ago by
Amit
• 0
0
votes
2
replies
149
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
z_bahari
• 0
0
votes
1
reply
69
views
Perfoming clumping using ieugwasr package
LinkageDisequilibrium
genom
linka
GenomicDistributionsData
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
zoheir.alayash
• 0
2
votes
2
replies
107
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
3 days ago • updated 1 day ago
feather-W
• 0
0
votes
1
reply
79
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 1 day ago by
Gordon Smyth
50k • written 3 days ago by
Gerhard Thallinger
▴ 180
2
votes
2
replies
150
views
between lane normalization upper quantile
EDASeq
edgeR
4 days ago • updated 16 hours ago
elesofi
• 0
2
votes
3
replies
2.0k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 2 days ago by
ATpoint
★ 3.9k • written 23 months ago by
liqidong52
▴ 20
0
votes
1
reply
70
views
problem with ClusterRepro function
WGCNA
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
Antonio.Aubry
• 0
0
votes
2
replies
182
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 4 days ago by
Michael Love
41k • written 6 days ago by
gglatzer
• 0
0
votes
4
replies
292
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
Jad
• 0
2
votes
2
replies
135
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
4 days ago
Sabiha
▴ 20
0
votes
6
replies
245
views
DESeq2 filtering vs edgeR filtering
DESeq2
updated 5 days ago by
Gordon Smyth
50k • written 5 days ago by
fr8712ca-s
• 0
0
votes
2
replies
134
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 days ago • updated 4 days ago
Sam
▴ 10
0
votes
2
replies
119
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 days ago • updated 4 days ago
kcarey
• 0
1
vote
1
reply
127
views
i'm not getting any differentially expressed genes.
DESeq2
updated 6 days ago by
ATpoint
★ 3.9k • written 6 days ago by
Marilyn
• 0
2
votes
1
reply
144
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 6 days ago by
ATpoint
★ 3.9k • written 6 days ago by
hemantcnaik
• 0
0
votes
1
reply
117
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 6 days ago by
BioinfoMug
• 0
0
votes
1
reply
106
views
Exact same results in Diffbind with different normalization methods
DiffBind
6 days ago • updated 1 day ago
red_bricks
▴ 50
0
votes
0
replies
68
views
FELLA plotGraph function won't change the legend
FELLA
6 days ago
yuhang
• 0
0
votes
0
replies
68
views
medips-output
ngsReports
MEDIPS
6 days ago
subhiksha
• 0
0
votes
0
replies
58
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
6 days ago
bocsci11
• 0
0
votes
1
reply
176
views
Syntenet error in infer_syntenet() Error in blast_list[[1]] : subscript out of bounds
syntenet
updated 7 days ago by
Fabricio Almeida-Silva
▴ 40 • written 6 weeks ago by
Sujeevan
• 0
0
votes
1
reply
204
views
question about data processing for syntenet
syntenet
updated 7 days ago by
Fabricio Almeida-Silva
▴ 40 • written 10 weeks ago by
Sujeevan
• 0
0
votes
2
replies
213
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
18 days ago • updated 6 days ago
shepherl
3.8k
0
votes
4
replies
172
views
Error in classify_gene_pairs
syntenet
doubletrouble
7 days ago
hfyuan2016
• 0
0
votes
1
reply
88
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
maltethodberg
▴ 170
0
votes
0
replies
64
views
The graphical interface of FELLA doesn't work
FELLA
7 days ago
yuhang
• 0
0
votes
0
replies
75
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
7 days ago
jean-christophe.helbling
• 0
1
vote
1
reply
133
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 7 days ago by
ATpoint
★ 3.9k • written 8 days ago by
synat.keam
• 0
0
votes
3
replies
273
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 6 weeks ago by
pl23
• 0
0
votes
2
replies
239
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
11 days ago • updated 9 days ago
Viktor Thiel
• 0
0
votes
0
replies
88
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
10 days ago
Henry
• 0
0
votes
1
reply
128
views
Rcpp compilation error
Release
Rcpp
updated 10 days ago by
ATpoint
★ 3.9k • written 11 days ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
88
views
Rain error: invalid annotation of time points
rain
11 days ago
mpuli011
• 0
0
votes
0
replies
78
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
11 days ago
Felix
• 0
0
votes
1
reply
107
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2
scCITE-seq
updated 11 days ago by
ATpoint
★ 3.9k • written 11 days ago by
daiane.hemerichbrennan
• 0
45,400 results • Page
1 of 908
Recent ...
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Answer: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
If you include `0+` in the model formula, then the order of the batch and treatment factors in the model becomes important. You need `0+gro…
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
by
James W. MacDonald
65k
The main goal here is to map human gene symbols to something else, which you can use the `Orthology.eg.db` package to do. You could also us…
Comment: How can I compute AIC for MAST hurdle model fitted in the whole dataset?
by
rproendo
▴ 20
Hi OP, checking in to see if you found a solution to this issue. I'm also interested in using AICs to evaluate model fits in MAST.
Comment: padj-based gradient scale from barplot (clusterProfiler results) does not work p
by
Eva
▴ 10
Oh god, it is right, how I didn't realise before. I got confused with the scientific format of the numbers and I was in a loop for nothing.…
Comment: Downloading count matrix for full recount3 dataset
by
Leonardo Collado Torres
★ 1.0k
AFAIK it's not.
Votes
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
A: HLA genes missing from TxDb.Hsapiens.UCSC.hg38.knownGene
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
DESeq2 design with multiple factors
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