User: bharata1803

gravatar for bharata1803
bharata1803240
Reputation:
240
Status:
Trusted
Location:
Japan
Last seen:
1 month, 2 weeks ago
Joined:
3 years, 1 month ago
Email:
b**********@gmail.com

Posts by bharata1803

<prev • 195 results • page 1 of 20 • next >
0
votes
2
answers
201
views
2
answers
Comment: C: Enrichment analysis for custom set
... No, I mean not the gene set definition, but the gene list that I want to calculate the enrichment. In DAVID, we just need to paste the gene symbol right, but I thought in GSEA, we need to submit gene list that contains not only the gene symbol but also the p-value or TPM or FPKM or something else. ...
written 11 weeks ago by bharata1803240
0
votes
2
answers
201
views
2
answers
Comment: C: Enrichment analysis for custom set
... I thought GSEA need gene list with p-value, TPM, or FPKM, right? What I want is similar with DAVID, upload a list of genes and can upload background and then do the enrichment analysis. CMIIW ...
written 11 weeks ago by bharata1803240
1
vote
2
answers
201
views
2
answers
Enrichment analysis for custom set
... Hello, I want to ask if there is an API for doing enrichment analysis by submitting your own set. For example, I have 5 gene set, Set 1, Set 2, ..., Set 5. I have a list of gene, gene A,B,C,D. I want to calculate the enrichment of gene A,B,C,D in the Set 1, Set 2,.., Set 5. I know several API ...
enrichment gene-ontology written 11 weeks ago by bharata1803240 • updated 11 weeks ago by Leite200
0
votes
0
answers
162
views
0
answers
Comment: C: Comparing DEG result from different experiment
... Thank you, I just want to make sure it is make sense. I have several times compare DEG analysis using DESeq2 and Limma and edgeR with same dataset and they produce similar result. ...
written 12 weeks ago by bharata1803240
1
vote
0
answers
162
views
0
answers
Comparing DEG result from different experiment
... Hello all, So I have a simple question. Suppose I download 2 or more dataset from NCBI GEO. Those dataset come from different experiment especially the NGS machine. For example one of them use Illumina and others use Ion Torrent. My first question is, if I calculated each dataset separately for DE ...
rna-seq deg written 12 weeks ago by bharata1803240
0
votes
0
answers
176
views
0
answers
Comment: C: Comparison of Subsetting gene sets for enrichment analysis
... Well, the definition of better is subjective. For example, from what I have done, I got 80 significant enrichment result if I don't subset the DEG. From these 80, the top rows mostly are just general cell function. The relevant enrichment result that related to cancer is in the middle. But, if I sub ...
written 3 months ago by bharata1803240
0
votes
0
answers
176
views
0
answers
Comparison of Subsetting gene sets for enrichment analysis
... Hello, So, I am working on a method. From this method I can get a small subset of differentially expressed genes. I only get around ~100 genes compared to if I don't use any subsetting metjhod, around ~3000. From this result, I compare the enrichment analysis using Enrichr, DAVID, and other similar ...
enrichment rna-seq written 3 months ago by bharata1803240
0
votes
0
answers
238
views
0
answers
Comment: C: GDC TCGA Metadata no project ID available?
... This is the metadata that I downloaded manually from GDC and then use my own parser: [csv file][1] [1]: https://www.dropbox.com/s/kjkfy9h6j2f6a9y/metadata_gbm.csv?dl=0 ...
written 3 months ago by bharata1803240
0
votes
0
answers
238
views
0
answers
Comment: C: GDC TCGA Metadata no project ID available?
... I see. If it is from GDC, maybe you can compare if you download manually from the portal. You can see whether the project_id exists in the original json format or not, if you still curious though. ...
written 3 months ago by bharata1803240
0
votes
0
answers
238
views
0
answers
Comment: C: GDC TCGA Metadata no project ID available?
... Have you downloaded metadata from the GDC website itself? It is in the json format. ...
written 3 months ago by bharata1803240

Latest awards to bharata1803

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 10 weeks ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 3 months ago, created a question with more than 1,000 views. For JASPAR motifs download
Popular Question 3 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 3 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 5 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 5 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 5 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 7 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 8 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 8 months ago, created a question with more than 1,000 views. For p53 upregulated in cancer cell line
Popular Question 9 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 9 months ago, created a question with more than 1,000 views. For p53 upregulated in cancer cell line
Popular Question 10 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 10 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 11 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 11 months ago, created a question with more than 1,000 views. For p53 upregulated in cancer cell line
Popular Question 11 months ago, created a question with more than 1,000 views. For Ensembl Hg38 dna, dna_rm, and dna_sm
Popular Question 12 months ago, created a question with more than 1,000 views. For p53 upregulated in cancer cell line
Popular Question 15 months ago, created a question with more than 1,000 views. For Processng cuffnorm output
Popular Question 15 months ago, created a question with more than 1,000 views. For Count read with summarizeOverlaps result 0 for all sample
Scholar 22 months ago, created an answer that has been accepted. For A: How to visualize a set of sequence alignments that all have the same reference s
Popular Question 2.0 years ago, created a question with more than 1,000 views. For From cuffnorm to DESeq

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1520 users visited in the last hour