User: jmah

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jmah10
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3 years, 3 months ago
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j***@ualberta.ca

Posts by jmah

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Does Chromvar require bulk ATAC-seq?
... Thank you! That makes a lot of sense. I'm very new to this (if that wasn't obvious) and I really appreciate your help. ...
written 9 days ago by jmah10
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Comment: C: Does Chromvar require bulk ATAC-seq?
... erased and rephrased original q ...
written 9 days ago by jmah10
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Does Chromvar require bulk ATAC-seq?
... According to the Chromvar vignette (https://bioconductor.org/packages/release/bioc/vignettes/chromVAR/inst/doc/Introduction.html), "If analyzing single cell data, it can make sense to use peaks derived from bulk ATAC-seq". The wording is confusing. Do they mean use annotation of peaks defined by bul ...
chromvar scatac-seq atac-seq written 9 days ago by jmah10
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Comment: C: Chromvar for single cell ATAC seq
... That's a really thoughtful response. I didn't think of the consequences of assuming that clustering in one space may not correspond to clustering in another. In fact, I would need to check that by clustering by RNAseq and motifs, and seeing if those clusters overlap. Thanks for your help! You've gi ...
written 11 days ago by jmah10
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Chromvar for single cell ATAC seq
... I want to find the master transcription factors (the transcription factors that govern the highest number of genes) per cell type in my animal. I will have single cell ATAC-seq and single cell RNAseq data. I was thinking of using the RNAseq data to group cells into metacells, then finding the most h ...
chromvar single-cell atac-seq atac-seq written 11 days ago by jmah10 • updated 11 days ago by AidanQuinn30
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Comment: C: GO slimming to specific parent term
... Thanks that looks perfect! I'll give it a try :) ...
written 4 months ago by jmah10
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GO slimming to specific parent term
... GO slimming allows you to trace back a child GO term to a broader, parent term. Is there a package (preferably R) that allows you to choose which parent you want to trace back to? i.e. For a set of GO IDs, I want to find all the ones that fall under the umbrella of, for example, "transcription regul ...
parent child slimming gene ontology go written 4 months ago by jmah10 • updated 4 months ago by Jean-Karim Heriche21k
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Comment: C: Go Partition Database or another like tool
... I too am very interested in this. Preferably, I'm looking for an R package or other similar software package rather than an html site though. Any luck? If I find something I will post back and let you know. ...
written 4 months ago by jmah10
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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 9 months 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 months ago by jmah10

Latest awards to jmah

Popular Question 3 months ago, created a question with more than 1,000 views. For GO enrichment - interpreting broad terms
Popular Question 8 months ago, created a question with more than 1,000 views. For HMMER error: Unrecognized format with Pfam-A.hmm
Popular Question 8 months ago, created a question with more than 1,000 views. For GO enrichment - interpreting broad terms
Popular Question 2.4 years ago, created a question with more than 1,000 views. For HMMER error: Unrecognized format with Pfam-A.hmm
Scholar 2.6 years ago, created an answer that has been accepted. For A: HMMER error: Unrecognized format with Pfam-A.hmm

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