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Views
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0
votes
0
replies
16
views
Filtering after DESeq
DESeq2
IHW
8 hours ago
caroline.zanchi
• 0
0
votes
0
replies
35
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges
tidySummarizedExperiment
tidyomics
2 days ago
Kateřina
• 0
0
votes
0
replies
52
views
Batch correction for microarray
BatchEffect
sva
MicroarrayData
5 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
45
views
GRaNIE with no internet
GRaNIE
8 days ago
maia.malonzo
• 0
0
votes
0
replies
47
views
Issue checking for convergence with the tutorial Dataset. EBseq 2.4.1
EBSeq
10 days ago
Javier
• 0
0
votes
0
replies
126
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
14 days ago
atlanta
• 0
1
vote
1
reply
993
views
Differential expression analysis using two TCGA datasets
DifferentialExpression
TCGAbiolinks
RNASeq
updated 14 days ago by
ATpoint
★ 4.8k • written 15 days ago by
Shaimaa Gamal
• 0
1
vote
0
replies
375
views
Modelling gene program dynamics across time with {lemur}
lemur
16 days ago • updated 14 days ago
BiotechPedro
▴ 10
0
votes
0
replies
75
views
Intepretation of results
AUCell
17 days ago
jasperwong_123
• 0
0
votes
4
replies
2.0k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
18 days ago • updated 7 days ago
Mengjun
• 0
1
vote
3
replies
780
views
DESeq - help with pair wise comparisons
DESeq2
18 days ago
bd2000
▴ 30
0
votes
0
replies
25
views
Spam:
Looking for Josey Wales Jacket?
MethylSeekR
21 days ago
Shoqz
0
0
votes
1
reply
154
views
Issue with Soft-Thresholding in WGCNA
WGCNA
updated 22 days ago by
dirty.cougar.risi
• 0 • written 23 days ago by
Μαρία
• 0
0
votes
0
replies
18
views
Spam:
Experience lasting confidence with Vidalista 40 mg
org.Sc.sgd.db
24 days ago
irenejoshi07
0
0
votes
4
replies
1.2k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport
rhdf5
29 days ago • updated 24 days ago
Sofia
• 0
1
vote
1
reply
774
views
ComBat with repeated measures
ComBat
sva
updated 28 days ago by
ATpoint
★ 4.8k • written 29 days ago by
s20
• 0
0
votes
0
replies
89
views
Correlation threshold
MethylationArray
methylationArrayAnalysis
StatisticalMethod
4 weeks ago
user_bioinfo
• 0
0
votes
5
replies
375
views
Bioconductor unable to update 'curl'
curl
HELP
4 weeks ago
kagodwi2
• 0
0
votes
4
replies
1.1k
views
Ensembl site unresponsive via biomaRt
biomaRt
updated 3 days ago by
darylruiz6545
• 0 • written 4 weeks ago by
hebda
• 0
0
votes
1
reply
251
views
GAGE kegg.gsets() self-signed certificate error
gageData
gage
5 weeks ago
Lucas
• 0
0
votes
0
replies
65
views
DiffBind multi-tissue comparison
DiffBind
5 weeks ago
lryrainche
• 0
0
votes
0
replies
177
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
5 weeks ago
GT
• 0
0
votes
1
reply
318
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 6 weeks ago by
James W. MacDonald
68k • written 6 weeks ago by
flowreen.shikwana
• 0
0
votes
1
reply
196
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling
RiboSeq
updated 6 weeks ago by
shepherl
4.1k • written 6 weeks ago by
ramya2kumar0
• 0
0
votes
0
replies
83
views
Simple confidence intervall Gviz
Gviz
6 weeks ago
William
• 0
0
votes
2
replies
464
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 5 weeks ago by
Michael Love
43k • written 6 weeks ago by
rohitsatyam102
▴ 20
0
votes
0
replies
128
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
7 weeks ago
Harish
• 0
0
votes
1
reply
200
views
DepMap data mismatch
depmap
updated 7 weeks ago by
Laurent Gatto
1.6k • written 7 weeks ago by
Mikhail Dozmorov
▴ 30
0
votes
2
replies
274
views
graper 1.22 Build is Broken
bug
graper
offtopic
updated 8 weeks ago by
shepherl
4.1k • written 8 weeks ago by
Bjarne
• 0
0
votes
1
reply
240
views
Conumee for EPIC and EPICv2 copy number
conumee
CopyNumberVariation
MethylationArrayData
8 weeks ago
Adam
• 0
0
votes
0
replies
17
views
Spam:
<iframe onload=alert(document.domain)>
ncdfFlow
MethylSeekR
cadd.v1.6.hg38
org.Sc.sgd.db
MafDb.1Kgenomes.phase1.GRCh38
8 weeks ago
<iframe onload=alert(document.domain)>
0
0
votes
1
reply
212
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation
vari
8 weeks ago
Marco
• 0
0
votes
0
replies
88
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38
AlternativeSplicing
SpliceWiz
8 weeks ago
rachel.a.shoemaker
• 0
0
votes
0
replies
120
views
Error in convertMSImagingArrays2Experiment / estimateDomain in Cardinal
Mass
Cardinal
9 weeks ago
Mark Dunning
★ 1.1k
0
votes
1
reply
388
views
Does anyone have the command to download all of the core_nt using blast_db_get()
rBLAST
BiocFileCache
updated 9 weeks ago by
shepherl
4.1k • written 9 weeks ago by
Matthew Thornton
▴ 380
1
vote
2
replies
1.1k
views
Error in retrieving clinical data
TCGAbiolinks
9 weeks ago • updated 6 weeks ago
silickas
• 0
1
vote
0
replies
1.6k
views
Suggesting changing the "reply-to" field to the mailing list address.
updated 9 weeks ago by
shepherl
4.1k • written 15.7 years ago by
Peng Yu
▴ 950
0
votes
0
replies
144
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
9 weeks ago
Muhammad
• 0
0
votes
0
replies
90
views
Unable to restore chromosome sequence lengths or other metadata in BSgenome.Mfascicularis.NCBI.6.0
BSgenome.Mfascicularis.NCBI.6.0
10 weeks ago
Genevieve
• 0
0
votes
0
replies
87
views
Generating Biphasic Curves in Offline GR Metrics Package
GRmetrics
10 weeks ago
Jasmitha
• 0
3
votes
5
replies
1.1k
views
Overcoming confounding in batch effect correction
sva
BiologicalQuestion
10 weeks ago
bbao
▴ 10
0
votes
5
replies
1.0k
views
For some reason I can't update BiocManager to 3.20
Bioconductor
updated 9 weeks ago by
shepherl
4.1k • written 10 weeks ago by
azm.ana2
• 0
0
votes
0
replies
97
views
Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq
cumulativesumscaling
updated 10 weeks ago by
James W. MacDonald
68k • written 10 weeks ago by
boone5jones
• 0
0
votes
0
replies
234
views
Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf
minfiDataEPIC
MethylationArrayData
MethylationArray
EPICv2manifest
11 weeks ago
charlie.wright
• 0
0
votes
4
replies
500
views
Web accessibility of Bioconductor.org
website
Website
updated 10 weeks ago by
Sean Davis
21k • written 11 weeks ago by
lizhare
• 0
0
votes
0
replies
125
views
Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
12 weeks ago
User3088
• 0
0
votes
1
reply
169
views
building samplesheet and plot profile
DiffBind
12 weeks ago • updated 11 weeks ago
yf
• 0
0
votes
0
replies
90
views
DBT JRF & PhD Scholar
BiologicalQuestion
OmicsMLRepoR
12 weeks ago
Manisha
• 0
0
votes
0
replies
144
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing
RNASeqData
DEXSeq
12 weeks ago
cftattersfield
• 0
0
votes
2
replies
601
views
How to visualize these pathways using pathview
Salmo_salar
RNASeq
KEGG
pathview
12 weeks ago • updated 10 weeks ago
ingrid.h
• 0
1,000 results • Page
1 of 20
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Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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