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0
votes
0
replies
15
views
DEseq2 to test half-life for time-series data
half-life
DESeq2
time-series
7 hours ago
Xianjun Dong
• 0
0
votes
1
reply
27
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
updated 10 hours ago by
Gordon Smyth
42k • written 18 hours ago by
jbono
• 0
0
votes
0
replies
23
views
RSamtools idxstats does not return unmapped reads
Rsamtools
15 hours ago
mja18
▴ 30
1
vote
2
replies
40
views
RSamtools idxstatsBam not working with remote bam file
Rsamtools
17 hours ago • updated 16 hours ago
mja18
▴ 30
0
votes
0
replies
17
views
Running > 100 samples per group - memory issues
xcms
memory
findchrompeaks
17 hours ago
abrsoule
▴ 30
0
votes
1
reply
37
views
CRISPRseek package: 5’ PAM?
CRISPRseek
updated 19 hours ago by
Julie Zhu
★ 4.3k • written 21 hours ago by
nderian
• 0
0
votes
0
replies
20
views
CAGEr consensusClustersDESeq2()
CAGEr
20 hours ago
MatteoP
• 0
0
votes
0
replies
19
views
CAGEexp vs CAGErseq
CAGEr
21 hours ago
MatteoP
• 0
0
votes
1
reply
27
views
Retrieve gene description with ensembldb
biomaRt
ensembldb
AnnotationData
updated 22 hours ago by
Johannes Rainer
★ 1.8k • written 23 hours ago by
António Miguel de Jesus Domingues
▴ 480
0
votes
2
replies
41
views
Outliers
outliers
Deseq2
1 day ago • updated 22 hours ago
nolwenn
• 0
0
votes
0
replies
17
views
Gviz: set colors for UTRs
plot
color
Gviz
utr
23 hours ago
ginlucks
• 0
0
votes
1
reply
27
views
Error in read.table function using multiclust
multiClust
updated 1 day ago by
Kevin Blighe
2.7k • written 1 day ago by
Debashis
• 0
0
votes
1
reply
29
views
log transformation the eset
codelink
updated 1 day ago by
Kevin Blighe
2.7k • written 1 day ago by
Yuxiii
• 0
3
votes
3
replies
77
views
Query regarding Differential gene expression analysis
limma
edgeR
DESeq2
2 days ago • updated 1 day ago
abhisekdey061
• 0
1
vote
4
replies
81
views
TCGA data analysis
RSEM
1 day ago
lily
▴ 20
0
votes
9
replies
250
views
How to setup sample design in DESeq2
DESeq2
6 weeks ago • updated 1 day ago
dequattro.concetta
▴ 10
0
votes
0
replies
33
views
Range value of the dispersion parameters (a1, alpha 0 and sigmad)
dispersion
DESeq2
polyester
2 days ago
catalina.gonzalez-gomez
• 0
2
votes
4
replies
57
views
BSGenome Forge for non-model organism
BSGenomeForge
BSGenome
updated 1 day ago by
Hervé Pagès
14k • written 2 days ago by
sieminsk
• 0
0
votes
3
replies
86
views
Issue loading data with tximeta
tximeta
updated 1 day ago by
Kevin Blighe
2.7k • written 3 days ago by
dshres
• 0
0
votes
6
replies
81
views
while doing co-expression network analysis, I am getting an error
RNASeqData
2 days ago • updated 1 day ago
Rishav
• 0
0
votes
1
reply
36
views
conumee (for EPIC): query intensities not given for all probes
IlluminaHumanMethylationEPICmanifest
minfi
conumee
updated 1 day ago by
Wang Yibo
• 0 • written 2 days ago by
theresa.walder
• 0
2
votes
4
replies
75
views
isSecondaryAlignment=FALSE with BWA MEM mapped BAM files not working?
bwa
Rsamtools
2 days ago • updated 1 day ago
sbcn
▴ 70
1
vote
12
replies
134
views
Data normalization
DESeq2
Normalization
2 days ago • updated 1 day ago
nolwenn
• 0
0
votes
1
reply
35
views
Deseq2 error "Error in designAndArgChecker"
DESeq2
updated 2 days ago by
Michael Love
32k • written 3 days ago by
polaxgr
▴ 10
2
votes
1
reply
64
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 3 days ago by
Rory Stark
★ 3.8k • written 4 days ago by
Sam
▴ 10
1
vote
1
reply
38
views
While I'm using edgeR how can I convert a .txt file and .tabular file into .RData file? please provide a code to completion of the process.
edgeR
updated 3 days ago by
Gordon Smyth
42k • written 3 days ago by
abhisekdey061
• 0
2
votes
2
replies
64
views
How do I set up a contrast matrix in edgeR with makeContrasts, when a relevant level was dropped?
edgeR
RNASeq
updated 3 days ago by
Gordon Smyth
42k • written 3 days ago by
Ryan
• 0
0
votes
2
replies
57
views
I want to use global test.
gene
r
clst
rpy
globaltest
3 days ago
Kim
• 0
0
votes
1
reply
74
views
CUT&Tag differential peak analysis using Diffbind, with pre-calculated normalization factor.
DiffBind
updated 3 days ago by
Rory Stark
★ 3.8k • written 4 days ago by
mwong043
• 0
2
votes
2
replies
120
views
A mismatch between DiffBind's results and the same results retreieved as DESeq2 (from DiffBind)
DiffBind
updated 3 days ago by
Rory Stark
★ 3.8k • written 19 days ago by
Sam
▴ 10
0
votes
0
replies
35
views
Run ViSEAGO with results fora
ViSEAGO
3 days ago
tim.meese
• 0
1
vote
8
replies
108
views
EPIC array single replicate pipeline?
minfi
methylationArrayAnalysis
4 days ago • updated 1 day ago
chay
• 0
0
votes
3
replies
57
views
Gviz featureAnnotation disappear when zooming in
Gviz
updated 20 hours ago by
James W. MacDonald
56k • written 4 days ago by
svenbioinf
• 0
1
vote
2
replies
45
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb
RNASeq
3 days ago
Torkel
• 0
1
vote
2
replies
46
views
Different genes using same method
DESeq2
3 days ago
menuka
• 0
0
votes
2
replies
48
views
champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis
EPICarray
ChAMP
Champ.SVD
4 days ago • updated 1 day ago
arisarkar88
• 0
2
votes
8
replies
119
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 3 days ago by
Gordon Smyth
42k • written 4 days ago by
Rishav
• 0
0
votes
0
replies
34
views
DECIPHER Package on dada2 -Implementing Silva_metaxa2 training set from qza file into a fastq.gz/.Rdata
DECIPHER
dada2
4 days ago
anrongloh
• 0
0
votes
0
replies
42
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
4 days ago
jbono
• 0
0
votes
6
replies
103
views
Error with hclust
dendrogram
hclust
textanalysis
R
RStudio
4 days ago • updated 1 day ago
Abby
• 0
0
votes
0
replies
32
views
News:
User handle changes to site
Bioconductor
handles
4 days ago
natay.aberra
10
3
votes
7
replies
115
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
updated 1 day ago by
Kevin Blighe
2.7k • written 4 days ago by
xiaofeiwang18266
▴ 20
0
votes
1
reply
47
views
News:
Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache
AnnotationHub
ExperimentHub
cache
4 days ago • updated 2 days ago
shepherl
2.6k
0
votes
0
replies
30
views
Summary CNV plot with conumee
conumee
4 days ago
melpag
• 0
0
votes
0
replies
34
views
Applying exomeCopy to call CNVs withouts controls considering batch effects
exomeCopy
CNV
WES
4 days ago
Cheng
• 0
1
vote
3
replies
67
views
How estimateDisp, glmQLFit and glmQLFTest process my TMM normalized read count matrix?
edgeR
glmQLFTest
glmQLFit
estimateDisp
updated 4 days ago by
James W. MacDonald
56k • written 5 days ago by
Giuseppe
• 0
0
votes
0
replies
36
views
Error when reading qPCR data in SDS format
HTqPCR
5 days ago
Nghia
• 0
0
votes
5
replies
117
views
DiffBind DEseq
DiffBind
updated 3 days ago by
swbarnes2
▴ 670 • written 6 days ago by
浩然
• 0
6
votes
1
reply
2.9k
views
Tutorial:
Accessing Public Genomic Data from Bioconductor
geoquery
geometadb
sradb
Tutorial
updated 6 days ago by
Ruban Rex
• 0 • written 5.9 years ago by
Sean Davis
21k
0
votes
2
replies
129
views
multifactorial design matrix
designmatrix
RNA-seq
limma
updated 6 days ago by
Gordon Smyth
42k • written 15 days ago by
athief
▴ 10
40,513 results • Page
1 of 811
Recent ...
Replies
Answer: Differential Transcript Usage: complex factorial design
by
Gordon Smyth
42k
edgeR does differential expression for transcripts via the catchSalmon function followed the usual edgeR pipelines as you would do for gene…
Comment: RSamtools idxstatsBam not working with remote bam file
by
mja18
▴ 30
Thanks Martin. Yes, that works.
Answer: RSamtools idxstatsBam not working with remote bam file
by
Martin Morgan
25k
Can you tell me if the following works for you? In a new R session ```{r} library(Rsamtools) setMethod(idxstatsBam, "BamFile", …
Comment: Aspli: error with gbCounts
by
achernomoretz
• 0
Hi Jeremy. We got it and we are working on the issue. Thanks for your patience. A
Comment: Aspli: error with gbCounts
by
jbono
• 0
Sorry, I forgot to respond here that I sent the file via email. Please let me know if you didn't receive it, thanks!
Votes
Answer: RSamtools idxstatsBam not working with remote bam file
Running > 100 samples per group - memory issues
R failing to load genome files from EnsDb.Hsapiens.v86
Comment: TCGA data analysis
Comment: BSGenome Forge for non-model organism
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