User: Ambika

gravatar for Ambika
Ambika40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
2 months, 3 weeks ago
Joined:
3 years, 4 months ago
Email:
a***************@gmail.com

Posts by Ambika

<prev • 117 results • page 1 of 12 • next >
0
votes
0
answers
140
views
0
answers
Error while mapping xml output from blast in Blast2GO
... Hello everyone, I am trying to do gene enrichment analysis on some predefined set of genes. For this I tried to annotate those genes against the swissprot and nr database. I tried to import the xml blast output (out format 5) in omics box. I was able to perform the mapping and GO annotation easily ...
blast2go mapping written 3 months ago by Ambika40 • updated 27 days ago by Biostar ♦♦ 20
0
votes
0
answers
141
views
0
answers
Comment: C: How to make KEGG plots based on the gene list with KO ID
... Can it interpret the KEGG ids and assign the pathways associated with it? ...
written 3 months ago by Ambika40
0
votes
0
answers
141
views
0
answers
How to make KEGG plots based on the gene list with KO ID
... Hello everyone, I do have file with gene list and corresponding KO Id from KEGG pathway analysis which looks like this: FUN_000082-T1 FUN_000109-T1 K00799 FUN_000143-T1 FUN_000188-T1 FUN_000231-T1 FUN_000233-T1 FUN_000387-T1 FUN_000399-T1 K00637 FUN_000399-T ...
keggorthology R plots written 3 months ago by Ambika40
0
votes
0
answers
309
views
0
answers
Comment: C: TopGO gene enrichment analysis with predefined set of genes for non-model organi
... Yes I want the p-values and the gene id (FUN__) in my results, which I am not getting. Thank you for the link, I will check that one. ...
written 3 months ago by Ambika40
0
votes
0
answers
309
views
0
answers
Comment: C: TopGO gene enrichment analysis with predefined set of genes for non-model organi
... Kevin, I think I do have a list as mentioned in the protocol. The list looks like this > head(gene2GO) $`FUN_000109` [1] "GO:0005515" "GO:0005515" "GO:0005515" "GO:0005515" $FUN_000399 [1] "GO:0008374" "GO:0008374" "GO:0008374" "GO:0008374" "GO:0008374" "GO:0008374" ...
written 3 months ago by Ambika40
0
votes
0
answers
309
views
0
answers
Comment: C: TopGO gene enrichment analysis with predefined set of genes for non-model organi
... Kevin, This is how my input files looks like: GO_total_upregulated_genes.csv GeneID Goterm FUN_004018 GO:0016491 FUN_004018 GO:0046872 FUN_004018 GO:0055114 FUN_003797 GO:0000287 FUN_003797 GO:0030976 FUN_003797 GO:0030976 FUN_00379 ...
written 3 months ago by Ambika40
2
votes
0
answers
309
views
0
answers
TopGO gene enrichment analysis with predefined set of genes for non-model organism
... Hello everyone, I am working with a non-model fungus and trying to do gene enrichment analysis for differentially expressed genes. For this I got the GO terms for a list of genes using InterProscan. Now I am using these list of genes with respective GO terms to do enrichment analysis and to make pl ...
R topgo rna-seq geneenrichment goterm written 3 months ago by Ambika40
0
votes
0
answers
255
views
0
answers
Comment: C: How to combine p-values of differentially expressed genes from different timepoi
... The program I am going to use does the hierarchical distribution based on p-value so I don't think I can do that. I need an exact p-value. ...
written 4 months ago by Ambika40
0
votes
0
answers
255
views
0
answers
Comment: C: How to combine p-values of differentially expressed genes from different timepoi
... I am doing gene enrichment analysis of differentially expressed genes using TopGO for which I need p-value of the listed genes. In my case I have 3 different p-values from three timepoints. I am looking for a way to combine these p-values to one so that I can proceed further. ...
written 4 months ago by Ambika40
1
vote
0
answers
255
views
0
answers
How to combine p-values of differentially expressed genes from different timepoints
... Hello everyone, I have the list of differently expressed genes from DESeq2 for three different timepoints. I have few genes that are differentially expressed in all three timepoints for which I want to combine the p-values to get one. I was thinking of taking an average p-value, but looks like that ...
p-value rna-seq written 4 months ago by Ambika40 • updated 10 weeks ago by Biostar ♦♦ 20

Latest awards to Ambika

Popular Question 3 months ago, created a question with more than 1,000 views. For HTseq error: Too few arguements
Popular Question 7 months ago, created a question with more than 1,000 views. For HTseq error: Too few arguements
Centurion 8 months ago, created 100 posts.
Popular Question 9 months ago, created a question with more than 1,000 views. For Cuffmerge error while merging gtf files
Great Question 9 months ago, created a question with more than 5,000 views. For Feature Counts output interpretation
Great Question 14 months ago, created a question with more than 5,000 views. For Unable to access jarfile trimmomatic-0.35
Popular Question 14 months ago, created a question with more than 1,000 views. For Interpretation of Results from trimmomatic
Popular Question 14 months ago, created a question with more than 1,000 views. For HTseq Pysam error
Popular Question 14 months ago, created a question with more than 1,000 views. For stranded vs not stranded Htseq-output differences
Popular Question 14 months ago, created a question with more than 1,000 views. For HTseq error: Too few arguements
Popular Question 17 months ago, created a question with more than 1,000 views. For Cufflinks gtf file to htseq
Popular Question 17 months ago, created a question with more than 1,000 views. For DESeq2 workflow for RNAseq
Supporter 18 months ago, voted at least 25 times.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Deseq2 library load error
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Unable to access jarfile trimmomatic-0.35
Popular Question 2.6 years ago, created a question with more than 1,000 views. For HTseq Pysam error
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Trimmomatic jar file
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Interpretation of Results from trimmomatic
Popular Question 2.6 years ago, created a question with more than 1,000 views. For HTseq error: Too few arguements
Popular Question 2.6 years ago, created a question with more than 1,000 views. For DESeq2 workflow for RNAseq
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Feature Counts output interpretation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Unable to access jarfile trimmomatic-0.35
Rising Star 3.2 years ago, created 50 posts within first three months of joining.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 934 users visited in the last hour