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Moderator: Jean-Karim Heriche

gravatar for Jean-Karim Heriche
Reputation:
22,860
Status:
Trusted
Location:
EMBL Heidelberg, Germany
Website:
http://jkh1.github.io/
Last seen:
56 minutes ago
Joined:
9 years, 2 months ago
Email:
h******@embl.de

Posts by Jean-Karim Heriche

<prev • 2,715 results • page 1 of 272 • next >
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Answer: C: heatmap in R
... The images you want to show are not linked. Also you seem to be plotting the log of the raw data. Try using the normalized counts instead or the log fold change since this is usually what we're interested in. Check the [DESeq2 vignette][1] section on heatmaps. [1]: https://bioconductor.org/pack ...
written 3 days ago by Jean-Karim Heriche ♦ 23k
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Comment: C: Does anyone else can explain the condition of revigo website?
... Have you tried contacting the developers/maintainers/authors? ...
written 20 days ago by Jean-Karim Heriche ♦ 23k
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Comment: C: Does anyone else can explain the condition of revigo website?
... I've moved your post to a comment as this is not an answer. ...
written 20 days ago by Jean-Karim Heriche ♦ 23k
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Answer: C: Known robust CRISPR KO effects on gene expression
... Related to robustness of the KO, you may also want to consider that cells often seem to find ways of re-expressing the knocked-out gene as [described in this paper][1] (and a couple others which I can't find now). [1]: https://www.nature.com/articles/s41592-019-0614-5? ...
written 5 weeks ago by Jean-Karim Heriche ♦ 23k
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Comment: C: How to identify cluster membership from the tSNE coordinates?
... I assume you're aware of [the pitfalls of clustering in t-SNE space][1]. This being said, it can be legitimate to want to identify which data point falls into which group, especially as part of exploratory data analysis. Since distances are not meaningful in t-SNE space, I would suggest using a dens ...
written 5 weeks ago by Jean-Karim Heriche ♦ 23k
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Comment: C: About SVD errors of big matrix
... This is not a bioinformatics question and there's not enough information. Memory not mapped means your process is trying to access memory it doesn't own. This is usually due to a bug however, it's unlikely you've found a bug in the LAPACK SVD (La.svd) so my guess would be that there's some conflict ...
written 6 weeks ago by Jean-Karim Heriche ♦ 23k
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Answer: A: file and directory management best practices
... Here is my take on [file-based data management][1] (initially written with microscopy image and derived data in mind but should be generally applicable). [1]: http://jkh1.github.io/data_management.html ...
written 6 weeks ago by Jean-Karim Heriche ♦ 23k
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Comment: C: I want to perform coresspondence analysis and calculate linear regression betw
... CA is typically applied to contingency tables. At the minimum, the data has to be positive and on the same scale. Standardization may achieve the latter but most likely introduces negative values. If your decimal data represent fractions then convert them to percentage or convert the percentages to ...
written 6 weeks ago by Jean-Karim Heriche ♦ 23k
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Answer: A: protein database peptide identification
... There are two options: - Map your peptides to a reference proteome - Search a database of previously reported peptides (e.g. [PRIDE][1], maybe try its [peptidome][2]) [1]: https://www.ebi.ac.uk/pride [2]: https://www.ebi.ac.uk/pride/peptidome ...
written 6 weeks ago by Jean-Karim Heriche ♦ 23k
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Comment: C: How to make a species co-occurrence network in Cytoscape?
... This question has its own [post here][1]. [1]: https://www.biostars.org/p/454866/ ...
written 6 weeks ago by Jean-Karim Heriche ♦ 23k

Latest awards to Jean-Karim Heriche

Scholar 10 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Librarian 4 weeks ago, created a post with more than 10 bookmarks. For Heatmaps in R
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Can someone give insight into the difference between current gene-function datab
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: How to make sure there is no duplicate sequence in a fasta file?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Can someone give insight into the difference between current gene-function datab
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 3 months ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Determination of hub genes in PPI network
Appreciated 4 months ago, created a post with more than 5 votes. For Graph visualization with igraph in R
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Appreciated 4 months ago, created a post with more than 5 votes. For Graph visualization with igraph in R
Appreciated 5 months ago, created a post with more than 5 votes. For Graph visualization with igraph in R
Appreciated 5 months ago, created a post with more than 5 votes. For Graph visualization with igraph in R
Scholar 5 months ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 5 months ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Scholar 5 months ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 5 months ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Scholar 6 months ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
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