Moderator: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe11k
Reputation:
10,760
Status:
Trusted
Location:
London/Brazil
Website:
https://github.com/kev...
Last seen:
8 hours ago
Joined:
4 months, 3 weeks ago
Email:
k**********@outlook.com

Posts by Kevin Blighe

<prev • 1,640 results • page 1 of 164 • next >
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Comment: C: NA for gff compare class code
... Thanks for posting more information! - Were the GTFs generated in the same way? - If you're also suppyling a reference GTF / GFF, is it the same as you used for aligning the files? - Are you using gffcompare from the old TopHat2 / Cufflinks packages or the upgraded HiSat2 / StringTie packa ...
written 8 hours ago by Kevin Blighe11k
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Comment: C: PCA from genotype data using the --pca option in plink2
... I believe that it is only done per chromosome in the interest of saving RAM. You can very easily do PCA on the entire dateset, too. Regarding LD pruning, it depends on what your end goals are. ...
written 22 hours ago by Kevin Blighe11k
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format
... If we just retain variants with low MAF, then every population (and sample) will be different because, by their very nature, low frequency variants are only present in a low number of samples. The algorithm 'fails' to find adequate relationships and then every sample is segregated from every other s ...
written 22 hours ago by Kevin Blighe11k
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Answer: A: How to find the hub genes in the gene co-expression network constructed by WGCNA
... One way: Convert the *WGCNA* object to an *igraph* object directly with wgcna2igraph, and then generate hub centrality scores via Kleinberg's metric, part of the *igraph* package. It does identify nodes/vertices that look like hubs visually when you inspect the graph. For further information about ...
written 1 day ago by Kevin Blighe11k
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Comment: C: How to root a tree in R with a polytomy at the root
... Glad that you got it sorted out. ...
written 2 days ago by Kevin Blighe11k
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Comment: C: Preprocessing Agilent Two-Color
... Why were you expecting it to segregate cases and controls? The type of clustering that you are doing is unsupervised, i.e., using all probe expression values; thus, it should never be expected that this will segregate your dataset as you desire. If you perform differential expression analysis betwe ...
written 2 days ago by Kevin Blighe11k
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Comment: C: Cuffmerge error(?) for RNA-seq
... Yep, well, you just need: PATH=/home/bioinfo/Downloads/cufflinks-2.2.1.Linux_x86_64:$PATH ...
written 2 days ago by Kevin Blighe11k
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Comment: C: Cuffmerge error(?) for RNA-seq
... Great - glad to have helped ...
written 2 days ago by Kevin Blighe11k
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Comment: C: Cuffmerge error(?) for RNA-seq
... Yes, you have to type that each time that you want to run Cufflinks (you can just include it as part of your code) - it is good practice to keep a separate script text file for each project on which you're working. Helps to be organised. More specifically, you should locate the directory in which t ...
written 2 days ago by Kevin Blighe11k
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Comment: C: RNA-Seq - Alignment GFF3/CDS against cluster (realised with CD-HIT)
... Can you assist by tidying your post somewhat? - thanks in advance. ...
written 2 days ago by Kevin Blighe11k

Latest awards to Kevin Blighe

Appreciated 21 hours ago, created a post with more than 5 votes. For A: pathogenicity predictors of cancer mutations
Teacher 21 hours ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Popular Question 21 hours ago, created a question with more than 1,000 views. For Produce PCA bi-plot for 1000 Genomes Phase III in VCF format
Scholar 3 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Scholar 3 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Scholar 7 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Appreciated 7 days ago, created a post with more than 5 votes. For A: pathogenicity predictors of cancer mutations
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Commentator 10 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Scholar 12 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Commentator 13 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Scholar 16 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Scholar 16 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Scholar 17 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Good Answer 18 days ago, created an answer that was upvoted at least 5 times. For A: pathogenicity predictors of cancer mutations
Scholar 21 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
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