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Showing :
questions
0
votes
0
replies
154
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
9 days ago by
Aspire
▴ 330
4
votes
3
replies
376
views
Demonstrating lack of difference between two peaksets
DiffBind
ChIP-seq
updated 7 weeks ago by
LauferVA
4.2k • written 7 weeks ago by
Aspire
▴ 330
10
votes
4
replies
518
views
6 follow
Doublechecking enrichment of promoters of DE genes
motifs
enrichment
updated 4 months ago by
ATpoint
82k • written 4 months ago by
Aspire
▴ 330
1
vote
3
replies
497
views
Consensus peaksets in DiffBind - conceptual questinos
DiffBind
updated 4 months ago by
Rory Stark
★ 2.0k • written 4 months ago by
Aspire
▴ 330
1
vote
5
replies
1.5k
views
What statistical test to apply for DE after CibersortX deconvolution
cibersortx
differential-expression
t-test
deconvolution
7 months ago by
Aspire
▴ 330
2
votes
2
replies
1.0k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
updated 17 months ago by
Sarah
• 0 • written 18 months ago by
Aspire
▴ 330
1
vote
1
reply
439
views
How to correctly apply -len/fragLength parameter in Homer's annotatePeaks.pl ?
homer
updated 18 months ago by
Matthias Zepper
4.6k • written 18 months ago by
Aspire
▴ 330
5
votes
2
replies
1.1k
views
How to avoid overfitting using SVA?
RNA-Seq
sva
overfitting
updated 22 months ago by
ATpoint
82k • written 3.6 years ago by
Aspire
▴ 330
5
votes
3
replies
1.2k
views
How to interpret similar motifs in Homer results
Homer
updated 24 months ago by
Mensur Dlakic
★ 27k • written 24 months ago by
Aspire
▴ 330
5
votes
2
replies
646
views
Why does DiffBind use the count of reads that fall within peaks?
DiffBind
updated 2.1 years ago by
Rory Stark
★ 2.0k • written 2.1 years ago by
Aspire
▴ 330
0
votes
0
replies
458
views
A question on Homer normalization
homer
updated 2.1 years ago by
ATpoint
82k • written 2.1 years ago by
Aspire
▴ 330
2
votes
1
reply
714
views
What is the correct order of flooring-normalization-batch correction for microarrays ?
microarray
updated 2.2 years ago by
Mohammad Rezaei
▴ 20 • written 2.2 years ago by
Aspire
▴ 330
0
votes
0
replies
369
views
Is there a public Yabi server available?
yabi
2.3 years ago by
Aspire
▴ 330
0
votes
0
replies
435
views
How to perform gene set enrichment analysis on genes that contribute to a specific PC?
pca
updated 2.4 years ago by
ATpoint
82k • written 2.4 years ago by
Aspire
▴ 330
0
votes
4
replies
1.2k
views
What is the precise range that Solexa quality scores can take?
phred
solexa
quality-score
fastq
2.5 years ago by
Aspire
▴ 330
3
votes
3
replies
1.2k
views
What QC measures to look for when performing deconvolution?
QC
CibersortX
deconvolution
updated 2.4 years ago by
Shicheng Guo
★ 9.4k • written 2.8 years ago by
Aspire
▴ 330
5
votes
6
replies
1.6k
views
How to check which genes affect a continuous phenotype
multiple-comparisons
multiple-regression
microarrays
regression
2.6 years ago by
Aspire
▴ 330
4
votes
3
replies
2.5k
views
Purpose of bamCoverage RPKM normalization method
rpkm
bamCoverage
updated 2.9 years ago by
ATpoint
82k • written 2.9 years ago by
Aspire
▴ 330
3
votes
11
replies
2.4k
views
Does DiffBind correctly designate peaks with very small fold-change to be significant
DiffBind
updated 2.9 years ago by
Rory Stark
★ 2.0k • written 3.3 years ago by
Aspire
▴ 330
0
votes
3
replies
1.1k
views
Cellular deconvolution intuition
deconvolution
3.0 years ago by
Aspire
▴ 330
2
votes
3
replies
744
views
Coverage required for 3' end RNA-seq methods
cel-seq2
updated 3.0 years ago by
Carlo Yague
8.7k • written 3.0 years ago by
Aspire
▴ 330
2
votes
6
replies
1.7k
views
A mismatch between DiffBind's results and the same results retreieved as DESeq2 (from DiffBind)
DiffBind
updated 3.1 years ago by
jared.andrews07
★ 16k • written 3.1 years ago by
Aspire
▴ 330
5
votes
8
replies
2.1k
views
What are the necessary and sufficient conditions for applying a multiple hypothesis correction?
multiple-comparisons
statistics
updated 3.0 years ago by
Jeremy Leipzig
22k • written 3.1 years ago by
Aspire
▴ 330
3
votes
3
replies
834
views
How can the assumption of a broad/narrow peak be checked?
macs2
ChIP-Seq
3.1 years ago by
Aspire
▴ 330
0
votes
2
replies
871
views
On understanding the axis of a PCA plot
pca
updated 3.2 years ago by
Sam
★ 4.7k • written 3.2 years ago by
Aspire
▴ 330
0
votes
0
replies
1.4k
views
Basic questions about Ngsplot heatmaps
ngsplot
heatmap
3.2 years ago by
Aspire
▴ 330
1
vote
0
replies
1.8k
views
Interaction terms and main effects in DESeq2
RNA-Seq
DESeq2
updated 3.3 years ago by
Biostar
20 • written 4.8 years ago by
Aspire
▴ 330
0
votes
3
replies
1.1k
views
Weird results in TopHat2 paired-end alignment
RNA-Seq
TopHat2
paired-end
updated 3.3 years ago by
Biostar
20 • written 3.6 years ago by
Aspire
▴ 330
2
votes
6
replies
2.6k
views
A question on the interpretation of a PCA plot
pca
updated 3.4 years ago by
rpolicastro
13k • written 3.4 years ago by
Aspire
▴ 330
5
votes
3
replies
1.3k
views
Why does it make sense to use gene symbols instead of gene ids in enrichment software?
enrichr
gene
updated 3.4 years ago by
igor
13k • written 3.4 years ago by
Aspire
▴ 330
0
votes
0
replies
592
views
How to understand the output of plotRap function in ChIPQC package?
ChIP-Seq
3.4 years ago by
Aspire
▴ 330
11
votes
7
replies
2.0k
views
Is there a reasonable way to rank peaks that are common between replicates?
ChIP-Seq
updated 3.4 years ago by
steve
★ 3.5k • written 3.4 years ago by
Aspire
▴ 330
1
vote
2
replies
1.2k
views
What could be the cause of different levels of binding in ChIP-Seq Input samples?
ChIP-Seq
ngsplot
updated 3.5 years ago by
Carlo Yague
8.7k • written 3.5 years ago by
Aspire
▴ 330
0
votes
4
replies
1.2k
views
Should the number of significantly DE genes rise with the number of SVs estimated (SVA package)?
sva
3.5 years ago by
Aspire
▴ 330
2
votes
6
replies
1.2k
views
Providing R1,R2 to macs2
ChIP-Seq
macs2
3.5 years ago by
Aspire
▴ 330
1
vote
1
reply
798
views
Clarifying the meaning of Bowtie2's default alignment mode (noob question)
bowtie2
updated 3.5 years ago by
Istvan Albert
100k • written 3.5 years ago by
Aspire
▴ 330
4
votes
5
replies
1.5k
views
RNA-SEQ where only a subset of genes is of interest
RNA-Seq
deseq
updated 3.6 years ago by
andres.firrincieli
3.6k • written 3.6 years ago by
Aspire
▴ 330
0
votes
3
replies
897
views
Tophat alignment and -g parameter
RNA-Seq
tophat
3.6 years ago by
Aspire
▴ 330
3
votes
1
reply
720
views
Htseq unable to process last read
RNA-Seq
htseq-count
3.7 years ago by
Aspire
▴ 330
2
votes
6
replies
868
views
How to choose the right model?
deseq2
RNA-Seq
glm
updated 3.7 years ago by
caggtaagtat
★ 1.9k • written 3.7 years ago by
Aspire
▴ 330
0
votes
4
replies
974
views
Usefulness of paired-end sequencing (noob question)
RNA-Seq
paired-end
tophat
3.7 years ago by
Aspire
▴ 330
5
votes
9
replies
2.3k
views
Paired end sequencing in case of a short biological insert
paired-end
RNA-Seq
3.7 years ago by
Aspire
▴ 330
7
votes
1
reply
1.6k
views
What is the importance of the rlog function (DESeq2) for downstream analysis?
deseq2
updated 3.9 years ago by
i.sudbery
19k • written 3.9 years ago by
Aspire
▴ 330
5
votes
5
replies
1.2k
views
Requirement of constant variance in limma-voom
voom
updated 3.9 years ago by
i.sudbery
19k • written 3.9 years ago by
Aspire
▴ 330
0
votes
4
replies
1.5k
views
What is the right way to convert probe names from Brainarray Custom CDF to Ensembl ?
custom-cdf
brainarray
affymetrix
microarray
3.9 years ago by
Aspire
▴ 330
4
votes
3
replies
1.9k
views
What could be a reason for peaks called via Macs2 not appearing as real peaks in IGV?
macs2
igv
updated 3.9 years ago by
ATpoint
82k • written 3.9 years ago by
Aspire
▴ 330
1
vote
1
reply
876
views
Should Affymetrix probe annotation include only specific gene biotypes?
microarrays
affymetrix
ensembl
updated 3.9 years ago by
Kevin Blighe
87k • written 3.9 years ago by
Aspire
▴ 330
0
votes
0
replies
1.2k
views
Why pileup values of MACS2 output have decimal values?
macs2
4.1 years ago by
Aspire
▴ 330
3
votes
11
replies
1.5k
views
Finding the cause for corrupt ChIP-Seq data
ChIP-Seq
updated 4.1 years ago by
colindaven
6.4k • written 4.1 years ago by
Aspire
▴ 330
7
votes
4
replies
2.5k
views
Aligning, Sorting and Converting to bam at the same command - possible?
alignment
sorting
bam
updated 4.3 years ago by
swbarnes2
14k • written 4.3 years ago by
Aspire
▴ 330
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