User: george.ry

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Posts by george.ry

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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 7 weeks ago by george.ry1.0k
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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 8 weeks ago by george.ry1.0k
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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 9 weeks ago by george.ry1.0k
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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 9 weeks ago by george.ry1.0k
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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 9 weeks ago by george.ry1.0k
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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 9 weeks ago by george.ry1.0k
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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 10 weeks ago by george.ry1.0k
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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 3 months ago by george.ry1.0k
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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 3 months ago by george.ry1.0k
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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 10 months ago by george.ry1.0k

Latest awards to george.ry

Guru 9 weeks ago, received more than 100 upvotes.
Scholar 9 weeks ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Scholar 9 weeks ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
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 13 months ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Scholar 21 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Pundit 2.1 years ago, created a comment with more than 10 votes. For C: Do bioinformaticians often break molecular biologists' hearts by being the first
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
Commentator 2.1 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 2.1 years ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 2.5 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 2.7 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Affymetrix Cel File - Probe Intensity Values To Rgb
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: How To Identify Quantile Normalized Expression Data
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: How To Identify Quantile Normalized Expression Data

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