User: alaincoletta

gravatar for alaincoletta
alaincoletta110
Reputation:
110
Status:
Trusted
Location:
Belgium
Last seen:
5 months, 2 weeks ago
Joined:
5 years, 8 months ago
Email:
a***********@insilicodb.org

about me

Posts by alaincoletta

<prev • 19 results • page 1 of 2 • next >
0
votes
1
answer
1.2k
views
1
answers
Comment: C: How to work with Deepvariant
... Sorry, I edited my reply and pointed to the pipeline source directly https://github.com/lifebit-ai/DeepVariant ...
written 5 months ago by alaincoletta110
1
vote
1
answer
2.4k
views
1
answers
Answer: A: Use a workflow management tool to manage your computational pipelines
... For Nextflow, I always recommend to anybody get started with implementations patterns. There is a really nice repository with plenty of examples: https://github.com/nextflow-io/patterns And maybe follow up with one of the workflows: https://nextflow-io.github.io/hack17-varcall/ This post shows ...
written 5 months ago by alaincoletta110
2
votes
1
answer
1.2k
views
1
answers
Answer: A: How to work with Deepvariant
... Hi [Vinay][1], we implemented the DeepVariant pipeline with Docker and Nextflow [here][2] [Lifebit][3] integrate it the pipeline with example parameters Would love your feedback on this. Thanks! [1]: https://www.biostars.org/u/40799/ [2]: https://github.com/lifebit-ai/DeepVariant [3]: ht ...
written 5 months ago by alaincoletta110
0
votes
1
answer
1.1k
views
1
answers
Answer: A: No function of Docker container for DeepVariant
... Hi Tobi, we implemented the DeepVariant pipeline with Docker and Nextflow [here][1] [https://lifebit.page.link/gnbR][2] . You can try it with example parameters. Would love your feedback on this. Thanks! [1]: https://lifebit.page.link/gnbR [2]: https://lifebit.page.link/gnbR ...
written 5 months ago by alaincoletta110
0
votes
1
answer
518
views
1
answers
Comment: A: deepvariant cannot import name locked_file
... Hi Mark, we implemented the DeepVariant pipeline with Docker and Nextflow [here][2] [Lifebit][3] integrate it the pipeline with example parameters Would love your feedback on this. Thanks! [1]: https://www.biostars.org/u/40799/ [2]: https://github.com/lifebit-ai/DeepVariant [3]: https:/ ...
written 5 months ago by alaincoletta110
0
votes
1
answer
518
views
1
answers
Comment: C: deepvariant cannot import name locked_file
... We implemented the DeepVariant pipeline with Docker and Nextflow. You can try it [here][1] [https://lifebit.page.link/gnbR][2] with example parameters. There is also a post with benchmarks across various AWS instances here: https://blog.lifebit.ai/post/deepvariant/. [1]: https://lifebit.page.l ...
written 5 months ago by alaincoletta110
1
vote
3
answers
2.3k
views
3
answers
Comment: C: Google announces DeepVariant
... We implemented the DeepVariant pipeline with Docker and Nextflow [here][2] [Lifebit][3] integrate it the pipeline with example parameters Would love your feedback on this. Thanks! [1]: https://www.biostars.org/u/40799/ [2]: https://github.com/lifebit-ai/DeepVariant [3]: https://lifebit.p ...
written 5 months ago by alaincoletta110
1
vote
5
answers
8.1k
views
5
answers
Answer: A: Heatmaps from cuffdiff output
... Here is a step-by-step tutorial. You can download public datasets with a report and step by step examples. https://insilicodb.com/differential-gene-expression-heatmap-from-rnaseq-data-using-cummerbund/ In InSilico DB, use the filters, on the left, to narrow your search to RNA-Seq data. Hope this ...
written 4.8 years ago by alaincoletta110
0
votes
7
answers
57k
views
7
answers
Answer: A: How To Draw A Heat Map For Gene Expression Data?
... Are you a bioinformatician or a biomedical researcher? If you are a Biomedical researcher I would recommend Gene-E from the Broad Institute to generate heatmaps, calculate differential gene expression and clusterings, and GenePattern (also from the Broad) to to perform more advanced analyses such a ...
written 4.8 years ago by alaincoletta110
0
votes
5
answers
3.6k
views
5
answers
Answer: A: Merging Datasets Together Using Excel
... InSilico DB has a "merging" R-Bioconductor package to combine public datasets from GEO and their clinical annotations. If you are not using R you can also combine data from the online platform (See this short step-by-step tutorial Example: # Retrieve 2 datasets eset1 = getDataset(gse="GSE10072", ...
written 4.9 years ago by alaincoletta110

Latest awards to alaincoletta

Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: How To Merge Two Microarrays Datasets?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2510 users visited in the last hour