User: jmah

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jmah10
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Posts by jmah

<prev • 21 results • page 1 of 3 • next >
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SynChro input files
... I'm trying to use SynChro, a program to analyze synteny. It uses CHROnicle to make 3 input files which it creates from Genbank .dat files or EMBL .embl files. I cannot find either of these files as provided by Genbank or EMBL. However, Genbank provides a .gbff file that seems to be the current "Gen ...
file conversion synchro written 26 days ago by jmah10
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SSE for Kmodes
... Is it possible to find the sum of squared errors for categorical data when using kmodes? Does this even make sense statistically for categorical data? ...
statistics written 11 weeks ago by jmah10
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Comment: C: Cluster plots from categorical clustering
... I'm not trying to analyze traditional expression-based single cell RNAseq data. I just put that in so people know it's a biology-based question. Sorry, I realize now that that was probably pretty confusing. ...
written 12 weeks ago by jmah10
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Cluster plots from categorical clustering
... Hi, I'm trying to analyze some single cell seq data. I have data set consisting of sets/groups of categorical data. eg. A { a,b,c,d} B {b,c,f,g} C {e,t,y,g} I have been trying to find an R package to cluster these eg. would A+B fall in the same cluster while C clusters separately? I envision som ...
R clustering written 12 weeks ago by jmah10
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Comment: C: GO enrichment - interpreting broad terms
... Thanks! I will look into topGO. It sounds pretty close to what I'm interested in. ...
written 20 months ago by jmah10
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Comment: C: GO enrichment - interpreting broad terms
... Thanks for pointing this out! ...
written 20 months ago by jmah10
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GO enrichment - interpreting broad terms
... Hi all, Looking at my GO enrichment analysis I see many very general terms eg. multicellular organismal process. How exactly does this get interpreted? Does this mean that the collection of proteins did not provide enough resolution to say that there was a more specific process going on? From a li ...
gene ontology go written 20 months ago by jmah10 • updated 20 months ago by Chirag Parsania1.4k
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Comment: A: OrthoMCL step 12: [mclxReadDimensions] could not parse header
... Hi Philipp and lu.ne, Thanks both of you for your advice! It looks like it works now with the -abc flag. Thank you very much for your help! ...
written 22 months ago by jmah10
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Comment: C: OrthoMCL step 12: [mclxReadDimensions] could not parse header
... And just for reference, here is the OrthoMCL manual which lists the steps I keep alluding to: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt Cheers, Jasmine ...
written 22 months ago by jmah10
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OrthoMCL step 12: [mclxReadDimensions] could not parse header
... Hi all, I'm having trouble with OrthoMCL step 12 (mlc command). I'm using a test set of two fastas with 10 proteins, five of which are identical to sequences in the other fasta. Thus, there should be five orthologs. All steps until step 12 appears to work. The orthologs.txt file in the pairs direct ...
orthomcl error written 22 months ago by jmah10

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Popular Question 19 months ago, created a question with more than 1,000 views. For HMMER error: Unrecognized format with Pfam-A.hmm
Scholar 22 months ago, created an answer that has been accepted. For A: HMMER error: Unrecognized format with Pfam-A.hmm

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