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 43k • written 5.2 years ago by • 0
9
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9
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6.7k
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Importing a BED file with floating point scores?
rtracklayer bed
updated 5.0 years ago by ▴ 150 • written 9.8 years ago by ★ 7.9k
0
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1
reply
1.8k
views
No gene can be mapped in Cluster profiler
clusterProfiler
updated 5.2 years ago by ★ 4.1k • written 5.2 years ago by • 0
0
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1
reply
1.2k
views
TPP and NPARC: A problem about the conversion of data frame.
TPP NPARC
updated 5.2 years ago by ▴ 20 • written 5.2 years ago by • 0
4
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5
replies
2.4k
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Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 8.3 years ago by ▴ 30
2
votes
3
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3.8k
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NCBI FTP server IP address
NCBI GEO
updated 5.2 years ago by • 0 • written 9.9 years ago by ▴ 10
3
votes
3
replies
1.7k
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se does not inherit from class SummarizedExperiment
DEP
5.2 years ago yueli7 ▴ 20
2
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6
replies
3.2k
views
Cannot download “EBImage” library in R
R EBImage
written 5.2 years ago by • 0
6
votes
3
replies
1.9k
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Annotating all SNVs in a genomic area, based on HG38 coordinates
Annotation variation HG38
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
6
votes
7
replies
2.4k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 5.1 years ago by 43k • written 5.2 years ago by ▴ 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 ▴ 360 • written 5.2 years ago by • 0
0
votes
1
reply
1.4k
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 5.2 years ago by ★ 29k • written 5.2 years ago by ▴ 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
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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 ▴ 360 • written 5.2 years ago by • 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 43k • written 5.2 years ago by ▴ 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 68k • written 5.2 years ago by • 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 ▴ 30 • written 5.2 years ago by ▴ 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 • 0 • written 5.2 years ago by ▴ 120
1
vote
6
replies
2.6k
views
Running FlowSOM in R problem
FlowSOM
updated 5.2 years ago by ▴ 10 • written 5.2 years ago by • 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 • 0 • written 5.2 years ago by • 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 ★ 29k • written 5.2 years ago by ▴ 40
2
votes
0
replies
1.1k
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News: BioC2021 organizing committee
BioC2021 S4Vectors
5.2 years ago Levi Waldron ★ 1.1k
0
votes
2
replies
983
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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 ★ 4.0k • written 5.2 years ago by ▴ 40
5
votes
4
replies
2.9k
views
edgeR supports continuous covariates?
edgeR
updated 3.0 years ago by • 0 • written 5.2 years ago by • 0
0
votes
3
replies
2.5k
views
edgeR::filterByExpr() returns unexpected result
edgeR
updated 5.2 years ago by 53k • written 5.2 years ago by • 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 43k • written 5.2 years ago by • 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 ★ 1.4k • written 5.2 years ago by • 0
1
vote
1
reply
3.4k
views
DMR Plot
dmr MethylationArrayData DMRcatedata
updated 5.2 years ago by 68k • written 5.2 years ago by • 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 ★ 5.2k • written 9.6 years ago by • 0
0
votes
2
replies
1.5k
views
DiffBind PE data
diffbind paired-end reads
updated 5.2 years ago by ★ 5.2k • written 9.0 years ago by ▴ 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 • 0 • written 7.5 years ago by ▴ 10
0
votes
2
replies
2.3k
views
DiffBind with highly variable FRiP (Fraction Reads in Peaks)
DiffBind
updated 5.2 years ago by ★ 5.2k • written 6.9 years ago by ▴ 20
2
votes
5
replies
1.7k
views
how to get the estimated libSize in DiffBind
diffbind
updated 5.2 years ago by ★ 5.2k • written 5.7 years ago by ▴ 40
1
vote
2
replies
1.1k
views
Can I completely repeat the DiffBind results using DESeq2?
diffbind
updated 5.2 years ago by ★ 5.2k • written 5.6 years ago by ▴ 40
1
vote
2
replies
1.2k
views
Using multiple covariates in DIffBind
DiffBind Deseq2
updated 5.2 years ago by ★ 5.2k • written 5.9 years ago by ▴ 10
1
vote
4
replies
2.7k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 5.2 years ago by ★ 5.2k • written 8.0 years ago by • 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 ★ 5.2k • written 6.2 years ago by ▴ 40
1
vote
8
replies
2.2k
views
Diffbind multiple blocking factor
diffbind rory stark chip seq
updated 5.2 years ago by ★ 5.2k • written 5.8 years ago by ▴ 10
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