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2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
18 hours ago by Aspire ▴ 330
0
votes
0
replies
182
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
28 days ago by Aspire ▴ 330
4
votes
3
replies
404
views
Demonstrating lack of difference between two peaksets
DiffBind ChIP-seq
updated 10 weeks ago by 4.2k • written 10 weeks ago by ▴ 330
10
votes
4
replies
564
views
6 follow
Doublechecking enrichment of promoters of DE genes
motifs enrichment
updated 4 months ago by 82k • written 4 months ago by ▴ 330
1
vote
3
replies
528
views
Consensus peaksets in DiffBind - conceptual questinos
DiffBind
updated 5 months ago by ★ 2.0k • written 5 months ago by ▴ 330
1
vote
5
replies
1.6k
views
What statistical test to apply for DE after CibersortX deconvolution
cibersortx differential-expression t-test deconvolution
8 months ago by Aspire ▴ 330
1
vote
1
reply
448
views
How to correctly apply -len/fragLength parameter in Homer's annotatePeaks.pl ?
homer
updated 19 months ago by 4.6k • written 19 months ago by ▴ 330
5
votes
2
replies
1.1k
views
How to avoid overfitting using SVA?
RNA-Seq sva overfitting
updated 23 months ago by 82k • written 3.7 years ago by ▴ 330
5
votes
3
replies
1.2k
views
How to interpret similar motifs in Homer results
Homer
updated 2.0 years ago by ★ 27k • written 2.0 years ago by ▴ 330
5
votes
2
replies
661
views
Why does DiffBind use the count of reads that fall within peaks?
DiffBind
updated 2.1 years ago by ★ 2.0k • written 2.1 years ago by ▴ 330
0
votes
0
replies
465
views
A question on Homer normalization
homer
updated 2.2 years ago by 82k • written 2.2 years ago by ▴ 330
2
votes
1
reply
721
views
What is the correct order of flooring-normalization-batch correction for microarrays ?
microarray
updated 2.3 years ago by ▴ 20 • written 2.3 years ago by ▴ 330
0
votes
0
replies
377
views
Is there a public Yabi server available?
yabi
2.3 years ago by Aspire ▴ 330
0
votes
0
replies
445
views
How to perform gene set enrichment analysis on genes that contribute to a specific PC?
pca
updated 2.4 years ago by 82k • written 2.4 years ago by ▴ 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 ★ 9.4k • written 2.8 years ago by ▴ 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 3.0 years ago by 82k • written 3.0 years ago by ▴ 330
3
votes
11
replies
2.4k
views
Does DiffBind correctly designate peaks with very small fold-change to be significant
DiffBind
updated 3.0 years ago by ★ 2.0k • written 3.4 years ago by ▴ 330
0
votes
3
replies
1.1k
views
Cellular deconvolution intuition
deconvolution
3.1 years ago by Aspire ▴ 330
2
votes
3
replies
765
views
Coverage required for 3' end RNA-seq methods
cel-seq2
updated 3.1 years ago by 8.7k • written 3.1 years ago by ▴ 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 ★ 17k • written 3.1 years ago by ▴ 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 3.1 years ago by 22k • written 3.1 years ago by ▴ 330
3
votes
3
replies
855
views
How can the assumption of a broad/narrow peak be checked?
macs2 ChIP-Seq
3.2 years ago by Aspire ▴ 330
0
votes
2
replies
878
views
On understanding the axis of a PCA plot
pca
updated 3.2 years ago by ★ 4.7k • written 3.2 years ago by ▴ 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 3.4 years ago by 20 • written 4.8 years ago by ▴ 330
0
votes
3
replies
1.1k
views
Weird results in TopHat2 paired-end alignment
RNA-Seq TopHat2 paired-end
updated 3.4 years ago by 20 • written 3.6 years ago by ▴ 330
2
votes
6
replies
2.6k
views
A question on the interpretation of a PCA plot
pca
updated 3.4 years ago by 13k • written 3.4 years ago by ▴ 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 13k • written 3.4 years ago by ▴ 330
0
votes
0
replies
596
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 3.5 years ago by ★ 3.5k • written 3.5 years ago by ▴ 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 8.7k • written 3.5 years ago by ▴ 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
3.6 years ago by Aspire ▴ 330
2
votes
6
replies
1.2k
views
Providing R1,R2 to macs2
ChIP-Seq macs2
3.6 years ago by Aspire ▴ 330
1
vote
1
reply
808
views
Clarifying the meaning of Bowtie2's default alignment mode (noob question)
bowtie2
updated 3.6 years ago by 100k • written 3.6 years ago by ▴ 330
4
votes
5
replies
1.5k
views
RNA-SEQ where only a subset of genes is of interest
RNA-Seq deseq
updated 3.7 years ago by 3.6k • written 3.7 years ago by ▴ 330
0
votes
3
replies
910
views
Tophat alignment and -g parameter
RNA-Seq tophat
3.7 years ago by Aspire ▴ 330
3
votes
1
reply
726
views
Htseq unable to process last read
RNA-Seq htseq-count
3.7 years ago by Aspire ▴ 330
2
votes
6
replies
893
views
How to choose the right model?
deseq2 RNA-Seq glm
updated 3.7 years ago by ★ 1.9k • written 3.7 years ago by ▴ 330
0
votes
4
replies
984
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
3.8 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 19k • written 3.9 years ago by ▴ 330
5
votes
5
replies
1.3k
views
Requirement of constant variance in limma-voom
voom
updated 3.9 years ago by 19k • written 3.9 years ago by ▴ 330
0
votes
4
replies
1.6k
views
What is the right way to convert probe names from Brainarray Custom CDF to Ensembl ?
custom-cdf brainarray affymetrix microarray
4.0 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 4.0 years ago by 82k • written 4.0 years ago by ▴ 330
1
vote
1
reply
881
views
Should Affymetrix probe annotation include only specific gene biotypes?
microarrays affymetrix ensembl
updated 4.0 years ago by 88k • written 4.0 years ago by ▴ 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 4.2 years ago by 6.4k • written 4.2 years ago by ▴ 330
7
votes
4
replies
2.5k
views
Aligning, Sorting and Converting to bam at the same command - possible?
alignment sorting bam
updated 4.4 years ago by 14k • written 4.4 years ago by ▴ 330
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