Showing : differential binding analysis • reset
4
votes
5
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2.0k
views
Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 7.1 years ago by ▴ 30
1
vote
3
replies
1.7k
views
Is there a way to run Diffbind without the normalization ?
diffbind differential binding analysis
updated 4.0 years ago by ★ 5.2k • written 6.3 years ago by ▴ 10
3
votes
2
replies
1.6k
views
diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 6.1 years ago by ★ 5.2k • written 6.1 years ago by • 0
0
votes
3
replies
1.2k
views
DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 6.2 years ago by 42k • written 6.2 years ago by ▴ 60
4
votes
7
replies
2.9k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 6.5 years ago by 42k • written 6.5 years ago by ▴ 20
4
votes
6
replies
1.8k
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 6.8 years ago by 42k • written 6.8 years ago by ▴ 60
0
votes
1
reply
945
views
Diffbind: How to compare the DBs called with and without a blocking factor
diffbind differential binding analysis blocking
updated 6.8 years ago by ★ 5.2k • written 6.9 years ago by • 0
2
votes
4
replies
1.7k
views
DiffBind report and MA-plot DB difference
diffbind differential binding analysis R report
updated 6.8 years ago by ★ 5.2k • written 6.9 years ago by • 0
2
votes
10
replies
3.9k
views
DESeq2 results export padj sorted
deseq2 deseq differential binding analysis
updated 6.8 years ago by 42k • written 6.8 years ago by ▴ 60
2
votes
4
replies
2.2k
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 6.8 years ago by ★ 3.8k • written 6.8 years ago by ▴ 60
2
votes
5
replies
1.5k
views
Mapping DESeq2 output back to chromosomal positions
deseq2 deseq diffbind differential binding analysis
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 60
2
votes
4
replies
1.3k
views
How to judge DESeq2_block and EdgeR_block result
diffbind Deseq2 edger differential binding analysis
updated 6.9 years ago by ★ 5.2k • written 6.9 years ago by • 0
4
votes
3
replies
1.4k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 6.9 years ago by ★ 28k • written 6.9 years ago by ▴ 60
9
votes
17
replies
2.0k
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 60
5
votes
6
replies
5.2k
views
Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
7.0 years ago Hesh ▴ 10
4
votes
7
replies
1.6k
views
Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 7.0 years ago by 42k • written 7.0 years ago by ▴ 60
2
votes
2
replies
921
views
Cleaning up DiffBind counts in relation to chromosome map
diffbind chipseq differential binding analysis
updated 7.0 years ago by ★ 5.2k • written 7.0 years ago by ▴ 60
4
votes
7
replies
1.6k
views
Altering design following DESeqDataSetFromMatrix and DESeq
deseq2 differential binding analysis
updated 7.0 years ago by 42k • written 7.0 years ago by ▴ 60
1
vote
2
replies
889
views
Pre-filtering DESeqDataSetFromMatrix input
deseq2 differential binding analysis
updated 7.1 years ago by 67k • written 7.1 years ago by ▴ 60
2
votes
1
reply
1.2k
views
Receiving error trying to import matrix into DESeq2
deseq2 deseq differential binding analysis
updated 7.1 years ago by ▴ 60 • written 7.1 years ago by ▴ 60
3
votes
3
replies
1.8k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
5
votes
7
replies
4.9k
views
Differential binding of ATAC-seq data with no replicates
ATAC differential binding analysis no replicates DEseq2 chromatin
7.7 years ago BioinfGuru ▴ 70
3
votes
9
replies
4.1k
views
DiffBind BED output with score
diffbind differential binding analysis
updated 7.8 years ago by ★ 5.2k • written 7.8 years ago by ▴ 60
3
votes
6
replies
2.1k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
3
replies
1.5k
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 8.3 years ago by ★ 28k • written 8.3 years ago by • 0
2
votes
1
reply
2.3k
views
DiffBind dba.analyze() to return all differentially enriched peaks?
diffbind p-value differential binding analysis fold enrichment values using diffbind
updated 8.4 years ago by ★ 5.2k • written 8.4 years ago by • 0
4
votes
1
reply
3.1k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 10
2
votes
1
reply
1.5k
views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ★ 7.9k
1
vote
1
reply
1.7k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 10
4
votes
2
replies
1.6k
views
Csaw : filter windows based on matched negative control
csaw differential binding analysis
9.1 years ago Pierre-François Roux • 0
1
vote
6
replies
6.1k
views
question about DiffBind
DiffBind differential binding analysis
updated 9.2 years ago by ★ 5.2k • written 9.2 years ago by • 0
31 results • Page 1 of 1
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Answer: Downloading Metagenomic Data with Higher Taxonomic Units by Levi Waldron ★ 1.1k
I'm sorry I missed the first post! Yes, it is easy to agglomerate ranks in curatedMetagenomicData datasets. See the example in the vignette…
Comment: Differene between the Wald and LRT test for time-series gene expression data by Denise • 0
This makes a lot of sense, thank you very much!
Comment: Downloading Metagenomic Data with Higher Taxonomic Units by elozanoe • 0
Hi! I'm facing the same problem. Is there any easy way to output relative abundances of higher taxonomic units (up to kingdom), similar to…
Comment: Is it recommended to analyze different tissues together when using edgeR by Gordon Smyth 51k
Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
Comment: Handling Epic Array Data by Melisa Tecik • 0
Thanks a lot for the help. You saved my day
Votes
A: correcting the batch effects in Limma and SVA
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
Answer: Differene between the Wald and LRT test for time-series gene expression data
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
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