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4
votes
4
replies
1.3k
views
visualization problem with BioMM package
BioMM
5.6 years ago
parra.sev
▴ 20
0
votes
0
replies
1.1k
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq
time series
5.6 years ago
Bogdan
▴ 670
0
votes
0
replies
1.0k
views
Error in data.frame(ASSIGN = "ASSIGN parameters", version = as.character(utils::packageVersion("ASSIGN")), : arguments imply differing number of …
software error
assign
5.6 years ago
yueli7
▴ 20
0
votes
1
reply
938
views
Which Package Should I Use to Predict Model Output Using RNA Seq Data?
regression
updated 5.6 years ago by
Gordon Smyth
53k • written 5.6 years ago by
theorist
• 0
0
votes
2
replies
2.8k
views
Error in taxa_are_rows(x) : trying to get slot "taxa_are_rows" from an object (class "otu_table") that is not an S4 object
deseq2
phyloseq
5.6 years ago
jaiber.solano.i
• 0
0
votes
1
reply
1.6k
views
DESeq2 normalization single cell
deseq2
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
ribioinfo
▴ 100
6
votes
2
replies
1.6k
views
tximport + edgeR not recommended?
tximport
edgeR
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
simon.michaelis88
• 0
2
votes
1
reply
1.4k
views
AnnotationHub errors when querying
annotation
updated 5.6 years ago by
Guido Hooiveld
★ 4.1k • written 5.6 years ago by
wewolski
▴ 10
1
vote
5
replies
3.8k
views
Error: Input Files have different Amount of Reads
SubRead
Align
Subjunc
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
abano
• 0
2
votes
6
replies
1.8k
views
Question: Method to get normalize allele specific read counts
edger
normalization
updated 5.6 years ago by
Aaron Lun
★ 29k • written 5.6 years ago by
hemantcnaik
• 0
1
vote
6
replies
6.6k
views
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
deseq2
rownames
updated 4.4 years ago by
Michael Love
43k • written 5.6 years ago by
corellig
▴ 10
0
votes
3
replies
2.2k
views
SummarizedExperiement extract assay with no name
deseq2
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
georgina.fqw
▴ 10
2
votes
8
replies
1.8k
views
Reason for NA in table after beta regression?
biseq
beta regression
5.6 years ago
akhaira
• 0
1
vote
3
replies
1.1k
views
Mixed-up column names for getBM()?
annotation
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
sarah.sandmann
• 0
0
votes
2
replies
771
views
Two data set: Control sample is one data set and Case is another data with Time-series
LIMMA
5.6 years ago
yuvayuvi369
• 0
2
votes
2
replies
1.7k
views
Tximport missing values for group summarizing counts
tximport
rat
reference
GTF
salmon
5.6 years ago
keremwai
• 0
1
vote
1
reply
1.1k
views
Is transcript color accessible through ensembldb? (gold = in both HAVANA+ENSEMBL)
ensembldb
updated 5.6 years ago by
Johannes Rainer
★ 2.1k • written 5.6 years ago by
Aditya
▴ 160
2
votes
4
replies
2.2k
views
Obtaining Comments From VCF Header
VariantAnnotation
VCFHeader
written 5.6 years ago by
Dario Strbenac
★ 1.6k
0
votes
8
replies
1.3k
views
Deseq2 weird values for Log2FC and pvalue.
deseq2
rnaseq
r
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
biom.andressa
• 0
1
vote
7
replies
2.1k
views
Question:Error installing BiocManager::install("org.Hs.eg.db") package.
software error
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
2211738718
• 0
6
votes
5
replies
1.6k
views
Security process for Bioconductor
software error
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
rhnewman
▴ 30
3
votes
3
replies
2.9k
views
EnsDb.Rnorvegicus for Rnor6
annotation
db
reference
rnor6
updated 5.6 years ago by
Guido Hooiveld
★ 4.1k • written 5.6 years ago by
keremwai
• 0
0
votes
1
reply
1.3k
views
mircomb analysis from deg's list
mircomb
mrna
mirna
degs
interaction
5.6 years ago
andreia
▴ 10
0
votes
2
replies
1.2k
views
mirna-mrna interation mircomb (from DEGs and DEMs lists)
deseq2
mircomb
degs
dems
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
andreia
▴ 10
12
votes
5
replies
5.6k
views
Rsamtools is not available for (for R version 4.0.2)
Rsamtools
updated 18 months ago by
Paul
• 0 • written 5.6 years ago by
yusuke_suita
▴ 40
4
votes
6
replies
2.0k
views
Extremely big genes in annotation TxDb packages
annotation
txdb
AnnotationData
Genetics
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
epibio
▴ 10
0
votes
3
replies
905
views
DESeq2 Design Model and Results Function Set-Up - How to know if using the interaction term is appropriate?
deseq2
rnaseq
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
gmchaput
• 0
0
votes
1
reply
1.1k
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu
RNASeq
DEXSeq
DESeq2
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
debatosh das
▴ 10
1
vote
3
replies
767
views
MAplots after lfcshrink
DESeq2
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
mc
• 0
0
votes
1
reply
1.8k
views
do expression of leading edges within a negative NES term reflect the same direction as it's enrichment score? aka downregulation of leading edges
fgsea
updated 5.6 years ago by
alserg
▴ 280 • written 5.6 years ago by
kavator
▴ 30
0
votes
0
replies
791
views
According to SCBN method, is it possible to acquire normalized data for virtualziation?
SCBN
normalization
5.6 years ago
tofukaj
• 0
5
votes
11
replies
2.4k
views
Visualization tool for GC-bias in SE data?
GC-bias
ALPINE
visualization
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
AKSR
▴ 20
2
votes
6
replies
2.0k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2
scran
batchelor
updated 5.6 years ago by
Aaron Lun
★ 29k • written 5.6 years ago by
Angelos Armen
• 0
1
vote
1
reply
961
views
A question for clarification regarding counts input to DESeqDataSetFromMatrix
deseq2
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
A
▴ 60
1
vote
2
replies
1.3k
views
EdgeR blocking factor - missing paired sample
EdgeR
edgeR
RNA-seq
differential expression analysis
blocking factors
updated 5.6 years ago by
Gordon Smyth
53k • written 5.6 years ago by
Lucy
▴ 60
0
votes
4
replies
3.0k
views
Error: unexpected string constant in "suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE)), when installed the package "Mus.musculus"…
install
packages
Mus.musculus
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
443606623
• 0
0
votes
0
replies
778
views
What values to include for predictedMethNull in BiSeq
Biseq
5.6 years ago
akhaira
• 0
0
votes
0
replies
1.3k
views
Job:
Senior Postdoc/Bioinformatician Research Fellow @ UEA, Norwich, UK - New deadline
cancer
nextgenerationsequencing
prostate
Job
5.9 years ago • updated 5.6 years ago
Daniel Brewer
▴ 100
4
votes
6
replies
3.2k
views
Using spike-in RNA for normalization of Salmon counts imported using Tximport
deseq2
Tximport
Sizefactors
normalizationfactors
spike-in
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
Hina Bandukwala
• 0
0
votes
0
replies
866
views
ViseaGO merge_enrich_terms ERROR
go
5.6 years ago
zaza.inline
• 0
0
votes
2
replies
14k
views
ComplexHeatmap - how to change the position of the legend of rowAnnotation
ComplexHeatmap
updated 8 months ago by
caroline.zanchi
▴ 10 • written 5.6 years ago by
AR3513
• 0
1
vote
1
reply
932
views
Obtain Protein-Protein Interaction (PPI) table from a list of Gene IDs in R or Python.
Protein Protein Interaction
Gene List
BioGRID
PICKLE
R Programming
5.6 years ago
omarrafiqued
▴ 50
1
vote
2
replies
1.9k
views
"Error in nbinomLRT(... less than one degree of freedom"... Isolating main and interaction effects with the LRT?
deseq2
main effects
interaction effects
R
lrt
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
laurenjfrazee
• 0
0
votes
9
replies
4.9k
views
WGCNA module trait relationship issue
wgcna
updated 5.6 years ago by
Peter Langfelder
★ 3.0k • written 5.6 years ago by
zen
• 0
7
votes
4
replies
2.5k
views
How does BiocParallel export variables to threads?
BiocParallel
SnowParam
parallel
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
gabriel.hoffman
▴ 170
1
vote
3
replies
1.8k
views
Package DECHIPER successfully downloaded but not installed
DECHIPER
unsuccessfull installation
updated 5.6 years ago by
kayla.interdonato
▴ 160 • written 5.6 years ago by
leahfa
• 0
4
votes
5
replies
1.8k
views
Custom Functional for automated DESeq2 running
deseq2
updated 5.6 years ago by
swbarnes2
★ 1.4k • written 5.6 years ago by
rekren
▴ 20
0
votes
2
replies
2.0k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview
ReactomePA
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
emisecherre
• 0
0
votes
2
replies
2.4k
views
DESeq2 doubts about transformations + nbinomWaldtest warning
rna-seq
deseq2
warnings
nbinomWaldTest
transformation
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
andreia
▴ 10
5
votes
9
replies
7.7k
views
Pipeline to analyzing Microarray data set( GSE files from NCBI GEO)
microarray
affy
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
adR
▴ 40
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