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0
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7
views
Do you like to drive or not?
NewWave
1 hour ago
aletheabrown051
• 0
0
votes
0
replies
25
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
6 hours ago
Gregory
• 0
0
votes
0
replies
21
views
Comparing RNASeq data from multiple studies
RNASeqData
RnaSeqSampleSize
RNASeqPower
RNASeq
8 hours ago
Luke
• 0
0
votes
1
reply
52
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 11 hours ago by
James W. MacDonald
63k • written 12 hours ago by
lin.pei26
• 0
0
votes
3
replies
67
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
updated 14 hours ago by
Mike Smith
★ 6.1k • written 1 day ago by
andrew.b.kleist
• 0
5
votes
2
replies
52
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
19 hours ago • updated 17 hours ago
Federico
▴ 10
0
votes
1
reply
113
views
error running exp2grn
NewWave
updated 18 hours ago by
Fabricio Almeida-Silva
▴ 40 • written 4 weeks ago by
adriana
• 0
0
votes
2
replies
45
views
Singlecell protein surface (ADT) pseudotime techniques
monocle
slingshot
20 hours ago
EspressoKris
▴ 10
0
votes
2
replies
49
views
shinyMethyl - saving the file
shinyMethyl
22 hours ago • updated 13 hours ago
dorota.komar
• 0
2
votes
4
replies
117
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData
DifferentialExpression
SmallRNAData
DESeq2
1 day ago • updated 7 hours ago
Shihui
• 0
0
votes
2
replies
72
views
Suggested package missing from Development version of Bioconductor
Devel
1 day ago • updated 21 hours ago
Richard
• 0
0
votes
0
replies
25
views
mixOmics with Bioconductor classes
mixOmics
1 day ago
Lluís Revilla Sancho
▴ 720
0
votes
0
replies
35
views
featureCounts error Assertion failed: (NULL == pairer -> bam_margin_table -> appendix2), function SAM_pairer_finish_margin_table, file input-files.c,…
NewWave
1 day ago
Kilian
• 0
0
votes
1
reply
73
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 1 day ago by
ATpoint
★ 3.4k • written 1 day ago by
Giuseppe
• 0
0
votes
0
replies
29
views
HTSeqGenie runs very slow
HTSeqGenie
2 days ago
zh9118
• 0
0
votes
0
replies
26
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno
ChIPSeq
MotifDiscovery
2 days ago
franciscrick41
• 0
5
votes
7
replies
223
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 2 days ago by
Gordon Smyth
48k • written 2 days ago by
Jonathan
▴ 10
0
votes
5
replies
121
views
DESeq2, results(dds, name = <reference>) interpretation results
DESeq2
2 days ago
Rockbar
• 0
0
votes
2
replies
108
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor
clusterProfiler
updated 2 days ago by
James W. MacDonald
63k • written 2 days ago by
nilanjanamani88
• 0
0
votes
1
reply
62
views
Create design matrix for differential methylation analysis
Annotation
annotate
DifferentialMethylation
minfiDataEPIC
updated 2 days ago by
Basti
▴ 720 • written 3 days ago by
titangerd
• 0
0
votes
1
reply
42
views
Specifying evidence channels in STRINGdb
STRINGdb
stringdb
3 days ago
robynne.braun
• 0
0
votes
0
replies
32
views
Variant Filtering on very large VCF files
VariantAnnotation
VariantFiltering
3 days ago
Bogdan
▴ 660
0
votes
3
replies
165
views
Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE
DESeq2
3 days ago
ruba-mahmoud
• 0
2
votes
2
replies
93
views
Remove duplicates of colData in TreeSummarizedExperiment
dplyr
TreeSummarizedExperiment
updated 3 days ago by
Michael Love
40k • written 3 days ago by
question_guy
• 0
0
votes
5
replies
138
views
DeSeq2 design fails (full model matrix is less than full rank)
DESeq2
updated 2 days ago by
James W. MacDonald
63k • written 3 days ago by
Theo
• 0
0
votes
2
replies
74
views
Adding chromosome numbers to the respective gene ids of DESeq2 output file
NewWave
hgu133a2.db
updated 3 days ago by
ATpoint
★ 3.4k • written 3 days ago by
roy23032
• 0
2
votes
6
replies
193
views
DataFrame Construction With Non-standard Column
S4Vectors
updated 3 days ago by
Hervé Pagès
16k • written 4 days ago by
Dario Strbenac
★ 1.5k
0
votes
0
replies
41
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
4 days ago
kthapa
• 0
0
votes
1
reply
103
views
''Model_Matrix'' error
DifferentialExpression
limma
updated 4 days ago by
Gordon Smyth
48k • written 5 days ago by
Laghalelle
• 0
0
votes
2
replies
2.9k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.2 years ago by
ag1805x
▴ 80
1
vote
3
replies
1.3k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 3.5 years ago by
hasse.bossenbroek
• 0
1
vote
3
replies
2.9k
views
SRAdb: Error downloading sqlite files
sradb
written 5.9 years ago by
arielle
• 0
0
votes
2
replies
518
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 2 hours ago by
aletheabrown051
• 0 • written 5 months ago by
mauricio.microbiol
• 0
2
votes
2
replies
981
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 2.8 years ago by
Dario Strbenac
★ 1.5k
0
votes
4
replies
1.5k
views
how to save subsetted GDS file
gwastools
written 5.4 years ago by
Adrienne Stilp
▴ 30
0
votes
1
reply
10k
views
heatmap.2 - change column & row locations; angle / rotate
Cancer
Cancer
written 9.9 years ago by
Cheng, Yong-Sheng
▴ 10
0
votes
2
replies
726
views
Rgraphviz installation: DLL problem?
Rgraphviz
Rgraphviz
written 13.7 years ago by
Gustavo Lacerda
▴ 10
1
vote
6
replies
2.2k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma
edger
timecourse
without replicate
voom
written 6.9 years ago by
Camila Orellana
▴ 10
1
vote
0
replies
46
views
News:
Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
db0
release
Annotation
6 days ago
kayla.interdonato
150
0
votes
0
replies
111
views
Huge effect of a single sample on DEGs
limma
6 days ago • updated 11 hours ago
Jonathan
▴ 10
0
votes
4
replies
183
views
filtering out lowly expressed genes by groups
RNASeqData
DESeq2
updated 6 days ago by
James W. MacDonald
63k • written 7 days ago by
sohail.mbio
▴ 10
0
votes
1
reply
86
views
Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
GEOmetadb
GEOmetadb.sqlite
dbConnect
updated 6 days ago by
James W. MacDonald
63k • written 6 days ago by
Lee
• 0
3
votes
4
replies
179
views
DMRcate design
Epigenetics
EpigeneticsWorkflow
DMRcate
6 days ago • updated 2 days ago
Jitendra
▴ 10
1
vote
1
reply
79
views
Further analysis after limma regression output
statistics
Epigenetics
limma
updated 6 days ago by
James W. MacDonald
63k • written 7 days ago by
Jitendra
▴ 10
1
vote
6
replies
358
views
DelayedArray::read_sparse_block
DelayedArray
updated 5 days ago by
Hervé Pagès
16k • written 5 weeks ago by
Koki
▴ 10
1
vote
2
replies
112
views
Manual creation of qPCRset does not work
bug
nondetects
HTqPCR
7 days ago
Ed Siefker
▴ 230
0
votes
3
replies
133
views
ukb Chromosomal position information was converted into SNPS
SNPediaR
updated 7 days ago by
James W. MacDonald
63k • written 8 days ago by
wenbo
• 0
1
vote
1
reply
85
views
Deseq2, enrichGO and ensembl ID
go
DESeq2
updated 7 days ago by
James W. MacDonald
63k • written 8 days ago by
Alvin
• 0
1
vote
4
replies
161
views
MDS plot edgeR
edgeR
updated 7 days ago by
Gordon Smyth
48k • written 8 days ago by
jbono
▴ 10
0
votes
10
replies
246
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware
ensembldb
updated 8 days ago by
James W. MacDonald
63k • written 8 days ago by
cjag
• 0
44,790 results • Page
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Comment: blockwiseModule crashes in the end and doesn't generate modules
by
aletheabrown051
• 0
Re: [drift boss][1] Have you fixed this problem yet? [1]: https://driftboss.io
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Shihui
• 0
It makes sense that DeSeq2 normalized FPMs are more accurate. Thank you for the information!
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
by
James W. MacDonald
63k
If you essentially combined multiple BAM files in the MACS call, you could then just combine them using `samtools cat`, in which case you o…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Michael Love
40k
I can rephrase your question as: Why is number of reads not the superior estimate for the scaling factor (the "m" in rpm). There are som…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Shihui
• 0
Hi Michael, Yes I manually calculated the RPMs by dividing each genes RPM to the library read depth. I didn't do any other normalization …
Votes
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Batch correction and Deseq2
A: Read counts between QSEA and MEDIPs
ComBat_seq function in sva package does not return a matrix
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