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User: macmath

gravatar for macmath
macmath • 140
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140
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France
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10 months, 2 weeks ago
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7 years, 8 months ago
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Posts by macmath

<prev • 62 results • page 1 of 7 • next >
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Answer: A: Empty output from MACS2 when using control
... 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 21 months ago by macmath • 140
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Answer: A: Visualize smooth ChIP peaks with Homer makeUCSCfile
... 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 21 months 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 22 months ago by macmath • 140
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Comment: C: How to filter subnetworks associated to specific cell type from human homo sapie
... I need to search inside encode for the cell type of my interest and do the needful... Thank you once again. ...
written 22 months ago by macmath • 140
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Comment: C: How to filter subnetworks associated to specific cell type from human homo sapie
... 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 22 months ago by macmath • 140
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How to filter subnetworks associated to specific cell type from human homo sapiens PPI network
... **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 ...
proteome ppinetwork written 22 months ago by macmath • 140 • updated 22 months ago by Jean-Karim Heriche ♦ 19k
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Comment: C: To get genes for each clusters from heatmap
... 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 23 months ago by macmath • 140
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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 23 months ago by macmath • 140
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Answer: A: Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
... 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 23 months ago by macmath • 140
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Answer: A: Is There A Webpage Or Server That Contains Data On Mouse Mitchondrial Genes Wit
... 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 23 months ago by macmath • 140

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