Showing : differential binding analysis • reset
4
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Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 7.6 years ago by ▴ 30
1
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4
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2.0k
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Is there a way to run Diffbind without the normalization ?
diffbind differential binding analysis
updated 7 weeks ago by • 0 • written 6.7 years ago by ▴ 10
3
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2
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1.7k
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diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by • 0
0
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3
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1.3k
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DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 60
4
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7
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Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 20
4
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6
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1.9k
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DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 60
0
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1
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1.0k
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Diffbind: How to compare the DBs called with and without a blocking factor
diffbind differential binding analysis blocking
updated 7.3 years ago by ★ 5.2k • written 7.3 years ago by • 0
2
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4
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1.8k
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DiffBind report and MA-plot DB difference
diffbind differential binding analysis R report
updated 7.3 years ago by ★ 5.2k • written 7.3 years ago by • 0
2
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10
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4.3k
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DESeq2 results export padj sorted
deseq2 deseq differential binding analysis
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 60
2
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4
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2.5k
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 7.3 years ago by ★ 3.8k • written 7.3 years ago by ▴ 60
2
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5
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1.6k
views
Mapping DESeq2 output back to chromosomal positions
deseq2 deseq diffbind differential binding analysis
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 60
2
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4
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1.4k
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How to judge DESeq2_block and EdgeR_block result
diffbind Deseq2 edger differential binding analysis
updated 7.4 years ago by ★ 5.2k • written 7.4 years ago by • 0
4
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3
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Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 60
9
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17
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2.2k
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DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 60
5
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6
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5.8k
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Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
7.4 years ago Hesh ▴ 10
4
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7
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1.8k
views
Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 60
2
votes
2
replies
979
views
Cleaning up DiffBind counts in relation to chromosome map
diffbind chipseq differential binding analysis
updated 7.4 years ago by ★ 5.2k • written 7.4 years ago by ▴ 60
4
votes
7
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1.7k
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Altering design following DESeqDataSetFromMatrix and DESeq
deseq2 differential binding analysis
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 60
1
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2
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968
views
Pre-filtering DESeqDataSetFromMatrix input
deseq2 differential binding analysis
updated 7.5 years ago by 68k • written 7.5 years ago by ▴ 60
2
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1
reply
1.3k
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Receiving error trying to import matrix into DESeq2
deseq2 deseq differential binding analysis
updated 7.5 years ago by ▴ 60 • written 7.5 years ago by ▴ 60
3
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3
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2.0k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
5
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7
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5.3k
views
Differential binding of ATAC-seq data with no replicates
ATAC differential binding analysis no replicates DEseq2 chromatin
8.1 years ago BioinfGuru ▴ 70
3
votes
9
replies
4.5k
views
DiffBind BED output with score
diffbind differential binding analysis
updated 8.2 years ago by ★ 5.2k • written 8.2 years ago by ▴ 60
3
votes
6
replies
2.3k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
0
votes
3
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1.8k
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Chip-seq analysis with input
chip-seq differential binding analysis
updated 8.7 years ago by ★ 28k • written 8.7 years ago by • 0
2
votes
1
reply
2.4k
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DiffBind dba.analyze() to return all differentially enriched peaks?
diffbind p-value differential binding analysis fold enrichment values using diffbind
updated 8.9 years ago by ★ 5.2k • written 8.9 years ago by • 0
4
votes
1
reply
3.3k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 10
2
votes
1
reply
1.7k
views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ★ 7.9k
1
vote
1
reply
1.8k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 9.1 years ago by ★ 28k • written 9.1 years ago by ▴ 10
4
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2
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1.7k
views
Csaw : filter windows based on matched negative control
csaw differential binding analysis
9.5 years ago Pierre-François Roux • 0
1
vote
6
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6.4k
views
question about DiffBind
DiffBind differential binding analysis
updated 9.6 years ago by ★ 5.2k • written 9.7 years ago by • 0
31 results • Page 1 of 1
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Replies
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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