Top new questions this week:
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"As a first step, we sought to systematically establish the complete set of genes implicated in the physiological response to SCI. We conducted a systematic analysis of the SCI literature, reviewing ...
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Is it faster to use the PySam package to run a python script on a bam
for read in samfile.fetch('chr1', 100, 120):
print read
compared to using a pipe and reading line by line from stdin in a ...
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I ran a calculation in RAxML to determine the majority consensus phylogeny of a maximum likelihood bootstrap (How to show bootstrap values on a phylogenetic tree constructed with RAxML), and I got ...
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after comments on my original post, I will ask my question again here
I have data (RNA expression values, obtained with multi-channel in situ hybridization) collected from 1mio human cells. For each ...
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I am a MSc student in Applied Biochemistry. For my Masters Thesis, I will be doing some research about finding new potent inhibitors for a specific enzyme of my choice using molecular docking (virtual ...
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This is the first time that I used lmfit function from the limma package and I'm a little bit confused on how to interpret the result. Also, is there a way to get the estimate or the beta from lmfit
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Greatest hits from previous weeks:
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How to extract the sequence used to create a blast database. This is useful when you download a blastdb from somewhere else e.g. one of the databases provided by NCBI including the 16SMicrobial ...
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I am writing a python script that requires a reverse complement function to be called on DNA strings of length 1 through around length 30. Line profiling programs indicate that my functions spend a ...
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Let $C$ be base coverage, $R$ is the length of reads and $K$ is the length of $k$-mer. Then $k$-mer coverage $C_k$ can be computed as $C_k = C\cdot(R - K + 1)/R$.
Could someone please explain why is ...
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I know that in Seurat we have the function CreateSeuratObject from which the analysis starts, but it accepts raw count matrix according to the documentation. I have only the already normalized count ...
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I would like to extract all the CDS from a batch of genomes. I have found a perl script from BioStars but this does not seem to work for me. I would preferably like to have a script/ method which will ...
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Well, I'm trying to convert a list of Human Gene referenced by Ensembl Gene IDs to Entrez Gene IDs. I have been advised to use biomart.
I tried to get a kind of conversion table for all human genes. ...
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This question has also been asked on biostars
How can I reproduce this volcano plot?
I'm only able to do the traditional one, I'm kind knew too these field.
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