User: Zhilong Jia
Zhilong Jia • 1.4k
- Reputation:
- 1,360
- Status:
- Trusted
- Location:
- London
- Website:
- http://zhilongjia.gith...
- Last seen:
- 12 hours ago
- Joined:
- 6 years, 8 months ago
- Email:
- v***@sina.com
a bioinformatician
Posts by Zhilong Jia
<prev
• 244 results •
page 1 of 25 •
next >
0
votes
2
answers
7.2k
views
2
answers
Comment:
C: Downloading Data From Mg-Rast
... http://api.metagenomics.anl.gov/metadata/export/mgp128
ref: http://api-ui.mg-rast.org/api.html#sample ...
written 6 months ago by
Zhilong Jia • 1.4k
0
votes
2
answers
7.2k
views
2
answers
Comment:
C: Downloading Data From Mg-Rast
... File 050.2 - This is the unfiltered metagenome that was originally uploaded to MG-RAST
File 100.1 - preprocess.passed.fna
File 100.2 - preprocess.removed (low quality)
File 350.2 & 350.3 - These are the protein coding genes (amino acids and nucleotides)
File 440.1 - These are ...
written 6 months ago by
Zhilong Jia • 1.4k
0
votes
1
answer
525
views
1
answers
... in line 4, it should be: ` foo <- data.frame(SampleType = paste0(rep(c("A","B"), each = 3)), Reps = rep(1:3, 2),` `Names = paste0(rep(c("A","B"), each=3), rep(1:3, 2) ) )`
`set.seed()` before generating the data will be helpful.
...
written 7 months ago by
Zhilong Jia • 1.4k
0
votes
1
answer
802
views
1
answers
Answer:
A: RNA-seq cluster analysis in R
... 0. [clusterProfiler][1]. [Visualization of profile comparison][2] section from Bioconductor package `clusterProfiler`. A quick solution for your question.
see ![figure][3].
1. [co-expressed gene set enrichment analysis, cogena][4]. `cogena` started with gene expression not clustered genes, While i ...
written 7 months ago by
Zhilong Jia • 1.4k
0
votes
3
answers
734
views
3
answers
... 0. [the toppcluster webserver][1], but not work recently.
1. [co-expressed gene set enrichment analysis, cogena][2]. But Zebrafish GO gene sets as a gmt file are needed.
2. clusterProfiler. `GO analyses (groupGO(), enrichGO() and gseGO()) support organisms that have an OrgDb object available.` so it ...
written 7 months ago by
Zhilong Jia • 1.4k
0
votes
0
answers
1.1k
views
0
answers
... 1. try to download it at the deployed website. you will see the downloaded files as follow.
![enter image description here][1]
2. `The expression profile data should be processed data, in which the fold change of one gene between group A and group B could be calculated with ValueA/ValueB`. Actually ...
written 7 months ago by
Zhilong Jia • 1.4k
2
votes
2
answers
2.2k
views
2
answers
... An enhancement : a function to transform the input matrix. ...
written 7 months ago by
Zhilong Jia • 1.4k
0
votes
1
answer
229
views
1
answers
Answer:
A: Heatmap2 code error
... Add `Colv=NA` to `heatmap.2(as.matrix(X), col=redgreen(75), scale="row", key=T, keysize=1.5, ` `density.info="none", trace="none",cexCol=0.9, labRow=NA, Colv=NA)`.
For detail, see manual of `gplots::heatmap.2`
BTW, see https://www.biostars.org/p/309884/ to get how to upload figures. `https://i.i ...
written 7 months ago by
Zhilong Jia • 1.4k
0
votes
0
answers
1.1k
views
0
answers
... Powerful. I will recommend to my colleagues. Two small bugs. 1. the try samples cannot be downloaded correctly. 2.heatmap cannot show negative value. BTW, how does it calculate the group expression per gene?
For 1. ![enter image description here][1]
For 2. ![enter image description here][2]
[1 ...
written 7 months ago by
Zhilong Jia • 1.4k
0
votes
3
answers
1.2k
views
3
answers
... I'm not familiar with python. It's a shame. However, I filed an issue at [github][1] and gave a simple solution that more tips during the poped inserting figure page. Thank you.
[1]: https://github.com/ialbert/biostar-central/issues/455 ...
written 7 months ago by
Zhilong Jia • 1.4k
Latest awards to Zhilong Jia
Popular Question
2 days ago,
created a question with more than 1,000 views.
For what does lowess smoothed line show in a MA plot
Popular Question
3 months ago,
created a question with more than 1,000 views.
For what does lowess smoothed line show in a MA plot
Popular Question
5 months ago,
created a question with more than 1,000 views.
For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Great Question
6 months ago,
created a question with more than 5,000 views.
For how to set the size of cell of heatmap.2 in R
Popular Question
7 months ago,
created a question with more than 1,000 views.
For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Popular Question
7 months ago,
created a question with more than 1,000 views.
For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Commentator
8 months ago,
created a comment with at least 3 up-votes.
For C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Popular Question
9 months ago,
created a question with more than 1,000 views.
For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Great Question
10 months ago,
created a question with more than 5,000 views.
For how to set the size of cell of heatmap.2 in R
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: How can we make this plot? (sequence logo)
Popular Question
10 months ago,
created a question with more than 1,000 views.
For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Popular Question
11 months ago,
created a question with more than 1,000 views.
For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Popular Question
12 months ago,
created a question with more than 1,000 views.
For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Student
14 months ago,
asked a question with at least 3 up-votes.
For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: How can we make this plot? (sequence logo)
Popular Question
15 months ago,
created a question with more than 1,000 views.
For How to calculate connectivity score for a compound in connectivity map O2?
Popular Question
16 months ago,
created a question with more than 1,000 views.
For A list of Bioinformatics projects for volunteers
Popular Question
16 months ago,
created a question with more than 1,000 views.
For How to calculate connectivity score for a compound in connectivity map O2?
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Epic Question
20 months ago,
created a question with more than 10,000 views.
For how to set the size of cell of heatmap.2 in R
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Great Question
2.4 years ago,
created a question with more than 5,000 views.
For how to set the size of cell of heatmap.2 in R
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1636 users visited in the last hour