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12
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Repeat CT in overrepresented sequences
ScRNA fastqc overrepresented sequences
1 hour ago by Analeigh • 0
0
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0
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29
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How to find the adapter sequence of an RNAseq dataset?
fastQC trimming adapter RNAseq
2 hours ago by Maryam • 0
0
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1
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131
views
Can a read be aligned more than once?
alignment gaf read sam
updated 11 hours ago by 146k • written 12 hours ago by ▴ 40
0
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0
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102
views
Is it possible to use multinichenet to find the targets of specific ligands coming from a specified cell type
multinicheNet CCI
19 hours ago by teofoskol • 0
0
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2
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237
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Inquiry about depth of coverage and copy number variation
number copy CNV sequencing depth variation
10 hours ago by Chen • 0
0
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1
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96
views
Magnesium ion in a post-docking adjustment
Docking Magnesium Ion
updated just now by ★ 2.5k • written 1 day ago by • 0
0
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2
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177
views
R encountering fatal error and quitting the session
R randomForestSRC Random-forest
16 hours ago by anjalivasudevan98 ▴ 40
0
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2
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189
views
Reconciling old crystallography papers with modern sequencing data
PDB proteomics
updated 19 hours ago by ★ 2.1k • written 2 days ago by ▴ 310
0
votes
2
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169
views
xCell output and immune cell ratio
statistics immunedeconv xCell
20 hours ago by a.stef.44 ▴ 10
0
votes
2
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235
views
Comparing GSEA mutant data to wild type
python gene GSEA R
7 hours ago by conmul • 0
1
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1
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339
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WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendrogram?
R genes transcriptomics WGCNA
updated 15 hours ago by • 0 • written 8 days ago by ▴ 10
0
votes
1
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265
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Statistical test to be used for dataset
biostatistics statistical-test
updated 12 hours ago by • 0 • written 20 days ago by ▴ 10
0
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1
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205
views
Genes of Interest in a Multi-Tissue Analysis
VST DGE DESeq2
updated 13 hours ago by • 0 • written 12 weeks ago by • 0
1
vote
1
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301
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Why does WGCNA use weighted correlation instead of Pearson correlation?
wgcna
updated 13 hours ago by • 0 • written 5 months ago by ▴ 10
0
votes
1
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277
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How can I determine the p-value of genes within each identified module in WGCNA?
WGCNA exportNetworkToCytoscape
updated 13 hours ago by • 0 • written 8 months ago by • 0
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Comment: Magnesium ion in a post-docking adjustment by dthorbur ★ 2.5k
[`AlphaFold3`](https://alphafoldserver.com/) (assuming you're not at conflict with their terms of use) can handle both ligands and ions. An…
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data by king • 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation by Chen • 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once? by GenoMax 146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset by allingt • 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap by jared.andrews07 ★ 18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type by allingt • 0
What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis by allingt • 0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
Comment: WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendr by allingt • 0
Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation? by allingt • 0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
Comment: dittoHeatmap; adding column labels on the heatmap by Varun Gupta ★ 1.3k
any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA? by allingt • 0
What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
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