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0
votes
0
replies
1.0k
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How to show rownames in densityheatmaps
ComplexHeatmap
5.2 years ago
adR
▴ 40
0
votes
3
replies
2.7k
views
Rsubread unable to return alignments
Rsubread
Alignment
updated 5.2 years ago by
Yang Liao
▴ 450 • written 5.2 years ago by
Daniel
• 0
1
vote
0
replies
1.2k
views
Job:
Computational Biologist at Denali Therapeutics
Biobase
biomarker
neuroscience
biotech
5.2 years ago
sandmann.t
▴ 70
0
votes
1
reply
2.5k
views
How to convert build 37 to build 38?
liftOver
updated 5.2 years ago by
shepherl
4.3k • written 5.2 years ago by
bluepebbles
• 0
0
votes
0
replies
927
views
Do p-values of Gene Significance per gene need to be FDR corrected?
WGCNA
5.2 years ago
Miguel.Cosenza
▴ 10
0
votes
4
replies
1.0k
views
Clarifying what results are returned by submitting a list of names to results() when using a user-specified matrix
DESeq2
5.2 years ago
thadryan
• 0
1
vote
0
replies
2.1k
views
News:
Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow
proteomics
Proteome
5.2 years ago
info
▴ 10
0
votes
0
replies
1.2k
views
How can I translate NM_xxx.y:c.xxG>C mRNA sequences to corresponding NC_xxx.y:g.xxxC>G chromosomal coordinates?
refseq
Bioconductor
conversion
5.2 years ago
heiko_kin
▴ 60
7
votes
2
replies
3.1k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 4.6 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 5.2 years ago by
Alexei Leliavski
▴ 60
2
votes
2
replies
918
views
Normalisation in DESeq2
DESeq2
Normalization
5.2 years ago
Bine
▴ 50
3
votes
2
replies
2.8k
views
Issue with AnnotationHub
AnnotationHub
5.2 years ago
rahnaman
▴ 10
7
votes
6
replies
5.2k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2
R
RNASeqR
5.2 years ago
ecg1g15
▴ 30
6
votes
6
replies
3.2k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2
VST
rsem
tximport
5.2 years ago
svlachavas
▴ 840
0
votes
7
replies
2.7k
views
Error report when loading a 0-byte bed file for DBA object in Diffbind
DiffBind
5.2 years ago • updated 5.0 years ago
ahua217
▴ 10
0
votes
2
replies
1.9k
views
Support for CSI indexes in Rsamtools
Rsamtools
5.2 years ago
bernatgel
▴ 150
0
votes
0
replies
1.2k
views
News:
Ensembl 102 has been released
Ensembl
biomaRt
BioMar
ensembldb
5.2 years ago
mchakiachvili
▴ 20
0
votes
1
reply
1.2k
views
DropletUtils::swappedDrops - Kallisto instead of CellRanger?
DropletUtils
updated 5.2 years ago by
Aaron Lun
★ 29k • written 5.2 years ago by
mhalache
• 0
5
votes
3
replies
4.3k
views
Gene conversion from SYMBOL to ENTREZ using AnnotationDbi doesn't convert some of the genes
AnnotationDbi
org.Hs.eg.db
5.2 years ago
Emilia
▴ 40
1
vote
5
replies
6.7k
views
RStudio vs R: using rtracklayer to import bigwig files from http works in R but not in RStudio.
import.bw
rtracklayer
http
RStudio
updated 5.2 years ago by
Michael Lawrence
★ 11k • written 5.2 years ago by
Søren
• 0
0
votes
2
replies
1.4k
views
Compining DESeq2 output with biomart query to display DE genes rather than DE ensembl IDs
DESeq2
updated 5.2 years ago by
James W. MacDonald
68k • written 5.2 years ago by
Linda
• 0
4
votes
7
replies
5.4k
views
DESeq2 DFrame error
DESeq2
updated 5.0 years ago by
Sara
• 0 • written 5.2 years ago by
Anna
▴ 20
4
votes
6
replies
2.3k
views
biomaRt "longer object length is not a multiple of shorter object length"
biomaRt
5.2 years ago
Linda
• 0
1
vote
2
replies
1.6k
views
BUG: `showOneDMR` from DSS package creates wrong axis labels
DSS
5.2 years ago
vi.hammer
• 0
2
votes
1
reply
1.0k
views
Possibility of multi-threading in "estimateDispersions" function
DESeq2
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
Hossein
• 0
0
votes
10
replies
2.9k
views
Error report when using dab() in Diffbind
DiffBind
5.2 years ago
ahua217
▴ 10
0
votes
11
replies
2.3k
views
Create `Copy Number Array' Data Object error
DNAcopy
5.2 years ago
El
• 0
9
votes
5
replies
5.5k
views
Normalise to a housekeeping gene in DESEq2
DESeq2
housekeeping
R
RNASeqData
5.2 years ago
ecg1g15
▴ 30
3
votes
6
replies
1.9k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2
RNASeqData
DifferentialExpression
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
Ben
▴ 50
0
votes
2
replies
1.1k
views
Extracting DESeq2 results when using a complex, user-specified matrix and post-hoc significance testing
DESeq2
5.2 years ago
thadryan
• 0
3
votes
1
reply
2.5k
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2
SingleCell
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
Christian
▴ 10
0
votes
1
reply
808
views
Different result when I run Deseq2 in terminal compare to Snakemake
DESeq2
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
David
• 0
0
votes
2
replies
1.4k
views
Effect of within-group variation on gene expression analysis
DESeq2
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
hpapoli
• 0
4
votes
3
replies
2.7k
views
Understanding DESeq2 contrasts and p-values
DESeq2
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
laura.baxter
▴ 30
8
votes
7
replies
13k
views
[DESeq2] Best way to select the optimal fitType for dispersion estimates?
deseq2
updated 5.2 years ago by
Michael Love
43k • written 9.8 years ago by
Christoph
▴ 10
0
votes
2
replies
2.5k
views
Cannot Install ShortRead Package
ShortRead
written 5.2 years ago by
Bob
• 0
1
vote
4
replies
2.0k
views
Errors when trying to install 'gwscat' on ubuntu with R 4.0.3
GWASTools
gwascat
updated 5.2 years ago by
Mike Smith
★ 6.6k • written 5.2 years ago by
wmov98
▴ 10
2
votes
0
replies
1.6k
views
How to liftOver Paired BED (bedpe) data
rtracklayer
5.2 years ago
Mikhail Dozmorov
▴ 30
1
vote
5
replies
1.8k
views
Is edgeR suitable for differential abundance of UNIref features from metatranscriptomics from HUMANnN2?
edgeR
HUMAnN2.0
5.2 years ago
Nick
• 0
2
votes
2
replies
829
views
Microarray
Bioconductor
5.2 years ago
mah.khansary
• 0
0
votes
0
replies
839
views
Expanded vcf
signeR
mutationcountmatrix
expandedvcf
5.2 years ago
Nikita
• 0
1
vote
2
replies
1.3k
views
How to load an expression matrix into Limma to perform Differential Expression Analysis.
limmaDEG
limma
updated 5.2 years ago by
Gordon Smyth
53k • written 5.2 years ago by
Pietro
• 0
0
votes
3
replies
2.2k
views
"genomdat must be numeric"error in DNAcopy Package (Solved)
DNAcopy
Varscan
updated 5.2 years ago by
El
• 0 • written 8.0 years ago by
jinxinhao1988
• 0
0
votes
0
replies
1.2k
views
Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE
hypeR
goTools
GOstats
topGO
5.2 years ago
Madza Farias-Virgens
• 0
1
vote
1
reply
1.8k
views
UniProt.ws - Speeding up select() for data retrieval
UniProt.ws
UniProt
updated 5.2 years ago by
James W. MacDonald
68k • written 5.2 years ago by
JavierM
• 0
0
votes
0
replies
1.3k
views
Job:
2 postdoc positions at Lund University, Sweden
CancerMutationAnalysis
AI
variationinterpreation
5.2 years ago
a1mauno
• 0
0
votes
0
replies
1.2k
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
5.2 years ago
Sam
▴ 10
1
vote
1
reply
1.3k
views
champ.DMP finds different probes in A-vs-B and B-vs-A analysis
DifferentialMethylation
ChAMP
champ.DMP
updated 5.2 years ago by
Yuan Tian
▴ 290 • written 5.2 years ago by
Ricardo
• 0
1
vote
9
replies
4.2k
views
How can I retrieve a protein's coding sequence using getSequence
biomaRt
5.2 years ago
heiko_kin
▴ 60
1
vote
2
replies
1.6k
views
Roast (fry) gene set testing with offset
EDASeq
edgeR
limma
5.2 years ago
gprezza
• 0
0
votes
0
replies
1.1k
views
Job:
Job: Product-focused Bioinformatician
massgeek
Reactome
Proteomics
STRINGdb
5.2 years ago
paula
• 0
46,730 results • Page
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Good point, I hadn't considered the fact quantitative `time` implies a (logit-)linear response *to* time. You're correct that I haven't exp…
Comment: Bile acid analysis with limpa
by
ATpoint
★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
Comment: chemmineOB install help
by
Jeremy
• 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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