User: george.ry

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george.ry1.1k
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Posts by george.ry

<prev • 96 results • page 1 of 10 • next >
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Answer: A: What is the actual cause of excessive zeroes in single cell RNA-seq data? Is it
... There's a variety of things at play here, but a few main things. Others can probably add some extra considerations. - Phased gene expression. RNA is not produced constantly and in an even manner. If I remember correctly, the idea of scRNAseq comes from studies of transcriptional regulation, rath ...
written 11 months ago by george.ry1.1k
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Answer: A: problem in fetching data using excel
... Get [datamash][1] ... it's invaluable! `sort -k1,1 < inputfile | datamash -g1 collapse 2 > groups` [1]: https://www.gnu.org/software/datamash/ ...
written 11 months ago by george.ry1.1k
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Comment: C: How do I generate all possible Newick Tree permutations for a set of species giv
... For how many leaf nodes then, outside of this example dataset? ...
written 11 months ago by george.ry1.1k
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Answer: A: Any alternative (free, open source tool) for Geneious software for phylogenetic
... You can also have a look at [UGENE][1] as an alternative to Geneious. [1]: http://ugene.net/ ...
written 11 months ago by george.ry1.1k
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Comment: C: How do I generate all possible Newick Tree permutations for a set of species giv
... Before you get too involved you need to make sure what you're planning is practical, as you get a lot of bifurcating trees from surprisingly few leaf nodes (and if it's bifurcating + others then it's even worse). If your plan is to do some compute for goodness of fit etc on all of these, then you m ...
written 11 months ago by george.ry1.1k
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Answer: A: Computing chunk of fasta file before moving to next chunks using python
... from collections import defaultdict as dd from Bio import SeqIO import numpy as np shuffles = dd(list) for record in SeqIO.parse(open('firstperm.fasta'), 'fasta'): id = record.id.split('_')[0] shuffles[id].append(len(record)) for k, v in shuffles.items( ...
written 11 months ago by george.ry1.1k
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Comment: C: How to Run the Script for Extracting Splice Sites from the Gene Annotation File
... This is technically an issue with a malformed GTF due to the GFF-->GTF conversion, rather than with the script per se - the GTF format is defined [here][1], and should always include `gene_id` and `transcript_id` (it should also end each line with a ';' character). It'll be simplest to just repl ...
written 11 months ago by george.ry1.1k
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Comment: C: Print line based on partial match
... It definitely will work, but you have to put `^` in front of the 5 letter sequences in `File1` ... ^ATGCC ^TTGCA ^GGAAC If you don't want to use grep then any program that will separate based on user-defined barcodes - flexbar / etc - will do this for you. ...
written 12 months ago by george.ry1.1k
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Answer: A: frequency of each nucleotide at each position in sequence
... If you're not looking to call the variants as Medhat says, then [bam-readcount][1] will do this. [1]: https://github.com/genome/bam-readcount ...
written 12 months ago by george.ry1.1k
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Answer: A: Run a Python program in Ubuntu
... This isn't your problem I don't think ... the package isn't handling it's own imports properly. You probably just need to change `from . import get_version` to `from GFFUtils import get_version`. The program isn't doing anything particularly exciting anyway, though, so you could also just do it in ...
written 20 months ago by george.ry1.1k

Latest awards to george.ry

Teacher 15 days ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Appreciated 5 months ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
Guru 11 months ago, received more than 100 upvotes.
Scholar 11 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Scholar 11 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Teacher 15 months ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 20 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Scholar 21 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Teacher 22 months ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
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Scholar 2.6 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
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Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
Commentator 2.8 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
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Appreciated 2.9 years ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 3.3 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Commentator 3.3 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Commentator 3.3 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 3.5 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
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