User: macmath
macmath • 140
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Posts by macmath
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... Could you check the parameter specifically based on the differences between regular peak vs broad peak
Example for **regular peak** calling: macs2 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01
Example for **broad peak** calling: macs2 callpeak -t ChIP.bam -c Control.bam --bro ...
written 2.2 years ago by
macmath • 140
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... You can try check the below parameters
Modifying Read Coverage
You can manually set the fragment lengths that are visualized and shift their positions, both of which can be useful:
-fragLength <# | given> : sets the fragment length, default: uses fragmentLengthEstimate in the tagInfo.txt file ...
written 2.2 years ago by
macmath • 140
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Comment:
A: interpretation Abyss stats
... Could you provide more details of the parameters used or any log information ...
written 2.3 years ago by
macmath • 140
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1
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... I need to search inside encode for the cell type of my interest and do the needful... Thank you once again. ...
written 2.3 years ago by
macmath • 140
0
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... Thank you for your suggestion. If I understood well the below flowchart is what you meant.
Example
GEO -> CD14 (human) ->Expression (How to fish out genes which are not expressed)
Kindly correct me if I am wrong. ...
written 2.3 years ago by
macmath • 140
1
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1
answer
652
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1
answer
... **I have been trying to filter the subnetwork associated with specific cells example CD14 from homo sapiens PPI network.**
How to **filter** from the homo sapiens **PPI network**?
So that the resulting network is **more specific** for CD14 cells.
And how to perform **unbiased validation** of the ...
written 2.3 years ago by
macmath • 140
• updated
2.3 years ago by
Jean-Karim Heriche ♦ 21k
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... Zhilong Jia can you suggest the way using two parameters `hclustfun` and `distfun` for clustering and then to get genes in clusters
Example matrix
KO1 KO2 KO3 KO4 WT1 WT2 WT3 WT4
ENSMUSG00000105261 1.9 ...
written 2.3 years ago by
macmath • 140
0
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1
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1.6k
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1
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Comment:
C: Heatmap for RNA-Seq data
... Can you provide me details of how you grouped them into clusters, because I wish to group my genes into cluster and also extract the gene set for each differentially bound clusters. ...
written 2.3 years ago by
macmath • 140
1
vote
2
answers
20k
views
2
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... The below lines provide also entrezgene id
require(biomaRt)
mart = useEnsembl("ENSEMBL_MART_ENSEMBL")
mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
bmIDs = getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id',
'description',
...
written 2.3 years ago by
macmath • 140
0
votes
5
answers
3.3k
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5
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... http://mitominer.mrc-mbu.cam.ac.uk/release-4.0/begin.do
MitoMiner, an integrated web resource of mitochondrial localisation evidence and phenotype data for mammals, zebrafish and yeasts. MitoMiner is now gene centric, with all data attached to gene objects ...
written 2.3 years ago by
macmath • 140
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