User: Abdullah

gravatar for Abdullah
Abdullah100
Reputation:
100
Status:
Trusted
Location:
Germany
Last seen:
2 years, 10 months ago
Joined:
6 years, 6 months ago
Email:
a**********@gmail.com

about me

Posts by Abdullah

<prev • 40 results • page 1 of 4 • next >
1
vote
1
answer
1.7k
views
1
answers
Comment: C: compare gene count profiles between samples
... FYI, The correlation did not yield the expected results. On the other hand, I tried RUVSeq and it seems to reduce the variability between the samples of the same cancer type quite nicely. I'm trying to use the PCA function as a method to see where my sample would fall in the PCA plot of each cancer ...
written 3.0 years ago by Abdullah100
0
votes
1
answer
1.7k
views
1
answers
Comment: C: compare gene count profiles between samples
... Thank you Devon. I thought correlation is too simple, but i will give it a try. do you suggest doing any kind of normalization or batch effect fixing? or directly perform the correlation on the TPMs? ...
written 3.0 years ago by Abdullah100
2
votes
1
answer
1.7k
views
1
answer
compare gene count profiles between samples
... Hi, I have a list of RNA-Seq from cancer samples to which I analyzed and generated the RPKM and TPM (calculated from RPKM) for all of the genes. Additionally, I downloaded a large set of public cancer samples (multiple cancer types) which I want to use as a comparison data and also generated the RP ...
rna-seq written 3.0 years ago by Abdullah100 • updated 2.9 years ago by Ar830
0
votes
1
answer
1.8k
views
1
answers
Comment: C: problem with KEGG pathway gene extraction
... The current version in git seems to be working now. Thanks ;) ...
written 3.5 years ago by Abdullah100
0
votes
1
answer
1.8k
views
1
answers
Comment: C: problem with KEGG pathway gene extraction
...  Thanks. The API example is working now. However, the command line tool still throw this error. It seems that the git is not updated? ...
written 3.5 years ago by Abdullah100
1
vote
2
answers
2.3k
views
2
answers
Answer: A: Ensembl gene ID conversion to gene name
... Have a look at http://mygene.info/. It is an efficiant way to make the conversion between Gene ID formats. It can be implemented inside a pipline as well. ...
written 3.5 years ago by Abdullah100
0
votes
2
answers
1.1k
views
2
answers
Answer: A: Multialignment of proteins sequences
... You might want to have a look at HMMER for your first request. ...
written 3.5 years ago by Abdullah100
0
votes
1
answer
1.8k
views
1
answers
Comment: C: problem with KEGG pathway gene extraction
... Thanks. When I run the API example, I get this error:   >>> df = get_kegg_data("rno", pathway_definitions) >>> Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2. ...
written 3.5 years ago by Abdullah100
0
votes
4
answers
1.7k
views
4
answers
Comment: C: the "major" problem of gene identifiers conversion
... We will be waiting for an update on the kg tool :) ...
written 3.6 years ago by Abdullah100
0
votes
4
answers
1.7k
views
4
answers
Answer: A: the "major" problem of gene identifiers conversion
... I came up with a weird solution to my problem. Not sure if this would help others. What I will do is the following: 1- download the GSEA KEGG lists (Entrez IDs) from here: http://www.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/5.0/c2.cp.kegg.v5.0.entrez.gmt . Howeve ...
written 3.6 years ago by Abdullah100

Latest awards to Abdullah

Student 3.6 years ago, asked a question with at least 3 up-votes. For problem with KEGG pathway gene extraction
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How To Align Then Visualize The Alignment Of Rna Sequences With R Or Python
Popular Question 4.2 years ago, created a question with more than 1,000 views. For How To Align Then Visualize The Alignment Of Rna Sequences With R Or Python

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1940 users visited in the last hour