User: macmath
macmath • 130
- Reputation:
- 130
- Status:
- Trusted
- Location:
- France
- Last seen:
- 6 months, 2 weeks ago
- Joined:
- 7 years, 4 months ago
- Email:
- m**********@gmail.com
Posts by macmath
<prev
• 62 results •
page 1 of 7 •
next >
0
votes
4
answers
2.2k
views
4
answers
... 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 17 months ago by
macmath • 130
0
votes
1
answer
882
views
1
answers
... 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 17 months ago by
macmath • 130
0
votes
2
answers
1.1k
views
2
answers
Comment:
A: interpretation Abyss stats
... Could you provide more details of the parameters used or any log information ...
written 18 months ago by
macmath • 130
0
votes
1
answer
501
views
1
answers
... I need to search inside encode for the cell type of my interest and do the needful... Thank you once again. ...
written 18 months ago by
macmath • 130
0
votes
1
answer
501
views
1
answers
... 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 18 months ago by
macmath • 130
1
vote
1
answer
501
views
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 18 months ago by
macmath • 130
• updated
18 months ago by
Jean-Karim Heriche ♦ 18k
0
votes
3
answers
4.3k
views
3
answers
... 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 19 months ago by
macmath • 130
0
votes
1
answer
1.1k
views
1
answers
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 19 months ago by
macmath • 130
0
votes
4
answers
17k
views
4
answers
... 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 19 months ago by
macmath • 130
0
votes
5
answers
3.1k
views
5
answers
... 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 19 months ago by
macmath • 130
Latest awards to macmath
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Which method could be used for cross normailizing microarray samples from different platforms namely (Affmetrix, Agilent,Illumina..) ?
Popular Question
16 months ago,
created a question with more than 1,000 views.
For How to create Correlation plots between wig files
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Removing Redundant Sequence Based On Genus Name
Popular Question
16 months ago,
created a question with more than 1,000 views.
For How to create Correlation plots between wig files
Supporter
18 months ago,
voted at least 25 times.
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For How to create Correlation plots between wig files
Popular Question
3.2 years ago,
created a question with more than 1,000 views.
For How to create Correlation plots between wig files
Popular Question
3.6 years ago,
created a question with more than 1,000 views.
For Extract Common Line Out Of Multiple Files
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1710 users visited in the last hour