User: Dirk

gravatar for Dirk
Dirk80
Reputation:
80
Status:
Trusted
Location:
Last seen:
3 weeks, 4 days ago
Joined:
8 years ago
Email:
s***********@gmail.com

Posts by Dirk

<prev • 16 results • page 1 of 2 • next >
0
votes
0
answers
86
views
0
answers
Comment: C: Gene enrichment or rescue dataset
... Perhaps worded slightly better--what I'm interested in would be something like a HT CRISPR-ish screen done in reverse, where in genes are systematically over-expressed, one by one ...
written 26 days ago by Dirk80
0
votes
0
answers
86
views
0
answers
Gene enrichment or rescue dataset
... I have a pipeline that incorporates a number of different data sets to identify a number of candidate genes as potential gene targets. However, I'm curious if there are publicly available data sets wherein either HTS of gene-rescue or over-expression studies have been performed (vs. control). My fir ...
crispr gene rna-seq written 26 days ago by Dirk80
0
votes
1
answer
342
views
1
answers
Comment: C: How to create own SRAdb
... There are some existing projects that are dependent on SRAdb being the in same format, e.g.: https://github.com/deweylab/MetaSRA-pipeline Is there a way to regenerate the SRAdb locally so that the code/data for MetaSRA can be updated, or is the bigquerty the only way forward? Cheers ...
written 4 months ago by Dirk80
0
votes
0
answers
341
views
0
answers
Comment: C: De Novo pathway generation
... I should note that my first idea is to create an adjacency matrix for each of the genes that use the weights of a neural network between the genes as the weights in the matrix and create an undirected acyclic graph from there, but wasn't sure if there was a better route. ...
written 13 months ago by Dirk80
0
votes
0
answers
341
views
0
answers
De Novo pathway generation
... I'm very interested in looking into a "de novo" generation of gene/protein interaction pathways that are built strictly from gene expression (e.g. rnaseq) datasets. I've looked around and have found that most of the work is done on gene enrichment or pathway enrichment, but I am very curious if we c ...
python rna-seq pathways written 13 months ago by Dirk80
0
votes
2
answers
656
views
2
answers
Comment: C: Obtaining GSM numbers from SRA ids
... Awesome, this looks like the best answer. It's a bit unfortunate you have to load a ~4GB file, but its still completely viable! ...
written 15 months ago by Dirk80
2
votes
2
answers
656
views
2
answers
Obtaining GSM numbers from SRA ids
... I have a lot of SRS values from the SRA values/ids for relevant entries in the SRA, and I would like to find the corresponding GSM ids that match to these. I can find them via the SRA webpage manually, but would really like a way to use curl or python (not R) to get these values--is that possible? ...
sra rna-seq written 15 months ago by Dirk80 • updated 12 months ago by Biostar ♦♦ 20
0
votes
0
answers
477
views
0
answers
Comment: C: Example of processed RNASeq datasets
... It doesn't *have* to be RNASeq, but that was my preference as there seems to be a plethora of data that exists for this platform, and the general consensus seems to be that its a more flexible approach that is more robust. I will definitely look at all of the microarray data, though. It functionally ...
written 18 months ago by Dirk80
0
votes
0
answers
477
views
0
answers
Comment: C: Example of processed RNASeq datasets
... The ultimate goal is to investigate general machine learning method performance on these datasets, as compared to popular programs/algorithms for gene/pathway enrichment programs (IPA, PANTHER, etc). Here, I mean to look into how read-counts for different genes are related to different phenotypes (e ...
written 18 months ago by Dirk80
0
votes
0
answers
477
views
0
answers
Example of processed RNASeq datasets
... I've found a number of informative tutorials on pipelines for processing RNASeq data, but can't seem to find any datasets or tutorials showing how to download or find RNASeq datasets (public) that have already been processed. I'm interested in a number of methods that need RNA expression matrices (e ...
rna-seq datasets written 18 months ago by Dirk80

Latest awards to Dirk

Good Question 13 months ago, asked a question that was upvoted at least 5 times. For Disease/Symptom Database
Appreciated 8.0 years ago, created a post with more than 5 votes. For Disease/Symptom Database
Great Question 8.0 years ago, created a question with more than 5,000 views. For Disease/Symptom Database
Epic Question 8.0 years ago, created a question with more than 10,000 views. For Disease/Symptom Database
Popular Question 8.0 years ago, created a question with more than 1,000 views. For Disease/Symptom Database
Student 8.0 years ago, asked a question with at least 3 up-votes. For Disease/Symptom Database

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1732 users visited in the last hour