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0
votes
0
replies
14
views
DEseq2 to test half-life for time-series data
half-life
DESeq2
time-series
7 hours ago
Xianjun Dong
• 0
0
votes
0
replies
23
views
RSamtools idxstats does not return unmapped reads
Rsamtools
15 hours ago
mja18
▴ 30
0
votes
0
replies
17
views
Running > 100 samples per group - memory issues
xcms
memory
findchrompeaks
16 hours ago
abrsoule
▴ 30
0
votes
0
replies
20
views
CAGEr consensusClustersDESeq2()
CAGEr
20 hours ago
MatteoP
• 0
0
votes
0
replies
19
views
CAGEexp vs CAGErseq
CAGEr
20 hours ago
MatteoP
• 0
0
votes
0
replies
17
views
Gviz: set colors for UTRs
plot
color
Gviz
utr
22 hours ago
ginlucks
• 0
0
votes
0
replies
33
views
Range value of the dispersion parameters (a1, alpha 0 and sigmad)
dispersion
DESeq2
polyester
1 day ago
catalina.gonzalez-gomez
• 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
0
votes
0
replies
35
views
Run ViSEAGO with results fora
ViSEAGO
3 days ago
tim.meese
• 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
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
41
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
4 days ago
jbono
• 0
0
votes
0
replies
30
views
Summary CNV plot with conumee
conumee
4 days ago
melpag
• 0
0
votes
0
replies
33
views
Applying exomeCopy to call CNVs withouts controls considering batch effects
exomeCopy
CNV
WES
4 days ago
Cheng
• 0
0
votes
0
replies
36
views
Error when reading qPCR data in SDS format
HTqPCR
5 days ago
Nghia
• 0
0
votes
0
replies
45
views
Annotation of downstream in ChIPseeker
downstream
Priority
ChIPseeker
8 days ago
Xiaojie Cheng
• 0
0
votes
0
replies
35
views
matchPattern function for multiple patterns in R
matchPattern
automatic
Biostrings
for-loop
8 days ago
adklts
• 0
0
votes
0
replies
32
views
Gviz import lor reads from bam file
Gviz
longreads
8 days ago
ginlucks
• 0
0
votes
0
replies
51
views
Error with Rhtslib
Rhts
Rhtslib
8 days ago
anand_mt
▴ 80
0
votes
0
replies
39
views
Extract flanking sequences SNP without reference genome
SNPData
snpStats
SNP
flankingsequences
9 days ago
Amber
• 0
1
vote
5
replies
142
views
while designing matrix i got an error, please help me out
RNASeqR
updated 10 days ago by
Basti
▴ 60 • written 10 days ago by
Rishav
• 0
0
votes
0
replies
72
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix
comBat
10 days ago
joannew
• 0
0
votes
0
replies
41
views
Blacklist error at dba.analyze(dbObj)
DiffBind
ChIPSeq
15 days ago
Goku
• 0
0
votes
0
replies
31
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
15 days ago
bioinfc
• 0
0
votes
1
reply
50
views
Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment
GenomicAlignments
17 days ago
Matthias Munz
• 0
0
votes
0
replies
31
views
Consensus wgcna soft threshold for each data
Transcriptomics
WGCNA
wgcna
18 days ago
2323982403
▴ 50
0
votes
2
replies
153
views
ChIPseeker failing on r-devel on CRAN checks
ChIPseeker
cinaR
20 days ago • updated 17 days ago
Onur Karakaslar
• 0
0
votes
0
replies
54
views
BiocParallel errors with xcms
BiocParallel
xcms
20 days ago
Yuki
▴ 10
0
votes
0
replies
38
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
20 days ago
jol.espinoz
▴ 40
0
votes
0
replies
34
views
NanoStringDiff - housekeeping genes variation
NanoStringDiff
20 days ago
YM
• 0
0
votes
0
replies
30
views
MSA package fails to be installed - installation of package ‘msa’ had non-zero exit status
msa
MultipleSequenceAlignment
20 days ago
thanos_docp
• 0
0
votes
0
replies
31
views
How to place jplace Querries from EPA RAxML on the tree as branches in Teeio/ggtree?
treeio
EPA
jplace
RAxML
ggtree
20 days ago
Vincent
• 0
1
vote
2
replies
93
views
Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 23 days ago by
Gordon Smyth
42k • written 23 days ago by
Rishav
• 0
0
votes
4
replies
126
views
DiffBind: dba.contrast for interaction terms
DiffBind
updated 3 days ago by
Rory Stark
★ 3.8k • written 23 days ago by
lindsaynhayes
• 0
0
votes
11
replies
218
views
Hello, I'm having trouble in installing Limma package and this is what Im getting
limma
updated 21 days ago by
Kevin Blighe
2.7k • written 23 days ago by
Deepti
• 0
1
vote
12
replies
152
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 7 days ago by
Vincent J. Carey, Jr.
6.3k • written 24 days ago by
naive
• 0
0
votes
0
replies
34
views
Issue with Implementing TSCAN
TSCAN
24 days ago
msu
• 0
0
votes
0
replies
37
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
24 days ago
el466
• 0
0
votes
2
replies
92
views
Visualising read alignments in
GenomicAlignments
Rsamtools
written 26 days ago by
Joshua
• 0
0
votes
0
replies
42
views
How can I download Methylation data for MethylMix package. (unusual error popped)
MethylMix
26 days ago • updated 24 days ago
Shloka Negi
• 0
0
votes
2
replies
88
views
I cannot install the splatter on colab
splatter
biocmanager
written 27 days ago by
Tianyu
• 0
0
votes
0
replies
52
views
Setting threshold with gage for gene set analysis
gage
gageData
28 days ago
jd348
• 0
0
votes
0
replies
50
views
Limma design multi-level experiment with 3 time points
R
proteomics
limma
29 days ago
ellen2270
• 0
0
votes
1
reply
68
views
Copy number Variation analysis using conumee
CopyNumberVariation
CopyNumberPlots
updated 29 days ago by
Kevin Blighe
2.7k • written 29 days ago by
shweta
• 0
0
votes
1
reply
70
views
when does the DOI become active?
CONSTANd
newpackage
updated 29 days ago by
shepherl
2.6k • written 29 days ago by
joris.vanhoutven
• 0
1
vote
4
replies
116
views
Failing to install DEP package. Some strange error.
R
Bioconductor
Install
DEP
4 weeks ago • updated 29 days ago
tpm
• 0
0
votes
0
replies
51
views
featureCounts running too long
RNAseq123
4 weeks ago
demirkalecy
• 0
0
votes
0
replies
51
views
Sample size on Differential Network Analysis
coexpression
WGCNA
4 weeks ago
Hanna
▴ 10
0
votes
4
replies
105
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics
DEP
4 weeks ago
rina
• 0
0
votes
0
replies
43
views
Gene network orientation grndata
grndata
4 weeks ago
stijn.hawinkel
• 0
11,278 results • Page
1 of 226
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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