User: evcon

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evcon10
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3 months ago
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Posts by evcon

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(Closed) create gsearesult object from gsea done outside of clusterprofilier
... I am using Absfiltergsea to perform gsea, is there a way to make a gsearesult object I can use in clusterprofilier to display the results? ...
R clusterprofilier gsea written 4 months ago by evcon10 • updated 4 months ago by Biostar ♦♦ 20
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Direction in GSEA in clusterProfiler
... Hi all, Im doing GSEA with the clusterProfiler package in R, and I have a question about direction. When Ive done gsea on other platforms there was a column saying whether the gene set was "up" or "down." I don't see this in the gsearesult object. So if the gene set GSE23321_CENTRAL_MEMORY_VS_NAIV ...
R rna-seq gsea written 5 months ago by evcon10 • updated 3 months ago by ugurcabuk130
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What is -e in trim_galore
... I was looking at the default settings for trim_galore! and I don’t know what -e means. From the manual -e Maximum allowed error rate (no. of errors divided by the length of the matching region) Default: 0.1 I get quality rimming, but I don’t understand what error rate could be ...
triming rna-seq written 10 months ago by evcon10 • updated 10 months ago by colin.kern920
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Job management programs
... I’m moving from a HPC that had slurm for job scheduling to one with no job management program. Is there a program that can sorta manage lots of parallel jobs kinda like personal slurm? I’m using screen but it’s kinda annoying, I’d like to start a lot of jobs and log off and come back later. ...
linux written 10 months ago by evcon10 • updated 8 months ago by Malte Petersen10
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How to use 0 and 1 coordinates in pyfaidx
... Im using pyfaidx to get genomic sequences, but I'm a little confused on the 0 vs 1 based coordinates. From the docs "Note that start and end coordinates of Sequence objects are [1, 0]. This can be changed to [0, 0] by passing one_based_attributes=False to Fasta or Faidx" So does that mean if I want ...
pyfaidx python written 2.1 years ago by evcon10 • updated 2.1 years ago by finswimmer13k
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Comment: C: genome sequence look up tool
... Thanks! This is perfect! Knew this had to exist already. ...
written 2.2 years ago by evcon10
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genome sequence look up tool
... Is there a tool to look up genomic sequences? Something in python would be most helpful. For example something like this: >>>getseq('chr1'.'100500','100505') AACTGC ...
genome sequence written 2.2 years ago by evcon10 • updated 2.2 years ago by h.mon31k

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