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0
votes
2
replies
906
views
Imbalanced samples on paired data using DESeq2
pairedsample
DESeq2
5.2 years ago
jeffsheng
• 0
0
votes
1
reply
2.1k
views
Rows do not converge in beta, labelled in mcols(object)$betaConv
DESeq2
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
Dana
• 0
9
votes
9
replies
6.7k
views
Importing a BED file with floating point scores?
rtracklayer
bed
updated 5.0 years ago by
merv
▴ 150 • written 9.8 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
1
reply
1.8k
views
No gene can be mapped in Cluster profiler
clusterProfiler
updated 5.2 years ago by
Guido Hooiveld
★ 4.1k • written 5.2 years ago by
Safina
• 0
0
votes
1
reply
1.2k
views
TPP and NPARC: A problem about the conversion of data frame.
TPP
NPARC
updated 5.2 years ago by
nils.kurzawa
▴ 20 • written 5.2 years ago by
yangwanqi
• 0
4
votes
5
replies
2.4k
views
Multi-factor blocking in DiffBind
diffbind
differential binding analysis
multiple factor design
written 8.3 years ago by
jared.andrews07
▴ 30
2
votes
3
replies
3.8k
views
NCBI FTP server IP address
NCBI GEO
updated 5.2 years ago by
SAn
• 0 • written 9.9 years ago by
maedakus
▴ 10
3
votes
3
replies
1.7k
views
se does not inherit from class SummarizedExperiment
DEP
5.2 years ago
yueli7
▴ 20
2
votes
6
replies
3.2k
views
Cannot download “EBImage” library in R
R
EBImage
written 5.2 years ago by
Henry1234
• 0
6
votes
3
replies
1.9k
views
Annotating all SNVs in a genomic area, based on HG38 coordinates
Annotation
variation
HG38
updated 5.2 years ago by
James W. MacDonald
68k • written 5.2 years ago by
Emanuele
• 0
6
votes
7
replies
2.4k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq
DESeq2
updated 5.1 years ago by
Michael Love
43k • written 5.2 years ago by
rohitsatyam102
▴ 20
1
vote
6
replies
2.1k
views
read.flowSet() raises " Argument 'phenoData' must be of type 'AnnotatedDataFrame'" error
flowCore
updated 5.2 years ago by
SamGG
▴ 360 • written 5.2 years ago by
Rainer
• 0
0
votes
1
reply
1.4k
views
improving running time of runNMF
runNMF
scater
singlecell
SingleCellExperiment
updated 5.2 years ago by
Aaron Lun
★ 29k • written 5.2 years ago by
lirongrossmann
▴ 50
0
votes
0
replies
1.1k
views
Which package I can use?
MSnbase
DAPAR
DEP
5.2 years ago
yueli7
▴ 20
3
votes
3
replies
9.6k
views
BiomaRt::getBM Error in UseMethod(filter_)
biomaRt
5.2 years ago
suyang
• 0
0
votes
3
replies
2.2k
views
Find DEPs among TMT labeling proteom time course data by limma
limma
proteomics
TMTlabeling
timecoursedata
updated 5.2 years ago by
SamGG
▴ 360 • written 5.2 years ago by
maleknias
• 0
0
votes
2
replies
1.3k
views
insufficient alignment
DECIPHER
Alignment
5.2 years ago
julius_vn
• 0
6
votes
8
replies
5.4k
views
Jitter p-values in volcano plot
EnhancedVolcano
DESeq2
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
philipp.rewe
▴ 20
0
votes
1
reply
2.2k
views
Adjust color of ellipse in PCA plot from DESeq2 data set
stat_ellipse
DESeq2
ggplot2
updated 5.2 years ago by
James W. MacDonald
68k • written 5.2 years ago by
thu.vo
• 0
0
votes
1
reply
1.7k
views
Waterfall failing with custom file: Error in `colnames<-`(`*tmp*`, value = c("sample", "gene", "trv_type")) : attempt to set 'colnames' on an obje…
variants
waterfall
GenVisR
updated 5.2 years ago by
zlskidmore
▴ 30 • written 5.2 years ago by
Jeni
▴ 10
0
votes
2
replies
3.4k
views
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
RSQLite
lumi
5.2 years ago
Rohmatul
• 0
0
votes
0
replies
838
views
[Function Request]converts a AA-based fasta alignment (that includes aa fasta sequences of different strains) into a vcf file
msa
5.2 years ago
yeli7068
• 0
0
votes
0
replies
1.3k
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage
rtracklayer
5.2 years ago
David
• 0
0
votes
3
replies
1.7k
views
Revisiting gene name inclusion in TxDB
Bioconductor
GenomicFeatures
TxDB
updated 4.2 years ago by
fabian.grammes
• 0 • written 5.2 years ago by
k.vitting.seerup
▴ 120
1
vote
6
replies
2.6k
views
Running FlowSOM in R problem
FlowSOM
updated 5.2 years ago by
sofie.vangassen
▴ 10 • written 5.2 years ago by
Václav
• 0
0
votes
3
replies
1.4k
views
HiCDCPlus / HiC-DC+ is not found
HiCDCPlus
HiC-DC+
HiCcompare
HiC
updated 3.7 years ago by
merve.sahn
• 0 • written 5.2 years ago by
mtS
• 0
0
votes
2
replies
1.4k
views
normalize the SILAC light heavy value
RforProteomics
5.2 years ago
yueli7
▴ 20
2
votes
7
replies
4.5k
views
How to run runNMF in parallel?
scater
single
SingleCellExperiment
updated 4.2 years ago by
Aaron Lun
★ 29k • written 5.2 years ago by
p.joshi
▴ 40
2
votes
0
replies
1.1k
views
News:
BioC2021 organizing committee
BioC2021
S4Vectors
5.2 years ago
Levi Waldron
★ 1.1k
0
votes
2
replies
983
views
vcfR2genlight error
genoset
5.2 years ago
Sakthipriya
• 0
0
votes
2
replies
1.5k
views
Can we align all the names of the transcripts (GeneRegionTrack) in the plotTracks() output?
Annotation
Alignment
Gviz
5.2 years ago
Vaibhav
• 0
0
votes
2
replies
1.3k
views
package ‘MSGFplus’ is not available (for R
MSGFplus
5.2 years ago
yueli7
▴ 20
1
vote
1
reply
888
views
Any possiblity applying
WGCNA
updated 5.2 years ago by
Kevin Blighe
★ 4.0k • written 5.2 years ago by
adR
▴ 40
5
votes
4
replies
2.9k
views
edgeR supports continuous covariates?
edgeR
updated 3.0 years ago by
Jeffcgen2000
• 0 • written 5.2 years ago by
Ivy
• 0
0
votes
3
replies
2.5k
views
edgeR::filterByExpr() returns unexpected result
edgeR
updated 5.2 years ago by
Gordon Smyth
53k • written 5.2 years ago by
Axel
• 0
0
votes
0
replies
1.0k
views
Job:
Two Fellowship Positions in Bioinformatics and Toxicology are avaiable immediately at US EPA
job
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
whduke
• 0
1
vote
2
replies
1.1k
views
DESeq2 with very large feature set
DESeq2
DifferentialExpression
5.2 years ago
ramiro.barrantes
▴ 10
1
vote
1
reply
801
views
What defines a batch in DESeq2 analysis
DESeq2
updated 5.2 years ago by
swbarnes2
★ 1.4k • written 5.2 years ago by
dhwanirupani92
• 0
1
vote
1
reply
3.4k
views
DMR Plot
dmr
MethylationArrayData
DMRcatedata
updated 5.2 years ago by
James W. MacDonald
68k • written 5.2 years ago by
Julie
• 0
0
votes
0
replies
1.4k
views
liftOver (R-package) how to recognize the "#Partially deleted in new" in the result ???
liftOver
5.2 years ago
geneprophet
• 0
0
votes
3
replies
1.4k
views
Is it possible in DiffBind to specify sizeFactors for DESeq2 analysis?
diffbind
normalization
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 9.6 years ago by
nfursova.msu
• 0
0
votes
2
replies
1.5k
views
DiffBind PE data
diffbind
paired-end reads
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 9.0 years ago by
rbronste
▴ 60
1
vote
4
replies
2.4k
views
Is there a way to run Diffbind without the normalization ?
diffbind
differential binding analysis
updated 11 months ago by
tifaGis
• 0 • written 7.5 years ago by
Thomas
▴ 10
0
votes
2
replies
2.3k
views
DiffBind with highly variable FRiP (Fraction Reads in Peaks)
DiffBind
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 6.9 years ago by
GFM
▴ 20
2
votes
5
replies
1.7k
views
how to get the estimated libSize in DiffBind
diffbind
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 5.7 years ago by
Guandong Shang
▴ 40
1
vote
2
replies
1.1k
views
Can I completely repeat the DiffBind results using DESeq2?
diffbind
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 5.6 years ago by
Guandong Shang
▴ 40
1
vote
2
replies
1.2k
views
Using multiple covariates in DIffBind
DiffBind
Deseq2
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
bioinfouser2
▴ 10
1
vote
4
replies
2.7k
views
MAnorm output as DiffBind input.
MAnorm
diffbind
normalization
chipseq
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 8.0 years ago by
ajeet
• 0
2
votes
4
replies
2.4k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind
Chipseq
spike-ins
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 6.2 years ago by
Konstantin Okonechnikov
▴ 40
1
vote
8
replies
2.2k
views
Diffbind multiple blocking factor
diffbind
rory stark
chip seq
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 5.8 years ago by
bioinfouser2
▴ 10
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