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5 votes

R packages for data analyses of pooled CRISPR screens

Assuming you mean CRISPR screens targeting many loci (for example using the GeCKO library) there is an R package here. It uses a linear mixed effect model to compare guide counts before and after a ...
3 votes
Accepted

How do I find the most similar sequences from a large set of short sequences?

130k * 20bp is a small data set. At this scale, SSE2 Smith-Waterman may work well: ...
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2 votes
Accepted

CRISPR Sequence Finder and Database Download

CRT (CRISPR Recognition Tool) http://www.room220.com/crt/ Crisprs Finder Online Tool https://crispr.i2bc.paris-saclay.fr/Server/ Piler-CR http://www.drive5.com/pilercr/ (Omic Tools List) https://...
2 votes

Large-scale gRNA design for a CRISPR screen

Perhaps GenomeCRISPR, I've personally never used it, but it has a well-documented API and appears you could automate it to go through the whole genome.
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2 votes

How do I find the most similar sequences from a large set of short sequences?

For this application, you could probably also do something like calculate the Hamming distances between all of the strings in an all-vs-all approach (it should not take too long or too much overhead). ...
1 vote
Accepted

Find CRISPR PAM-sites with python

The easiest solution is finditer ...
  • 8,035
1 vote

CRISPR screening and systems biology

To investigate genes through a network based approach you can use several tools. I don't know which level of programming you have or which tool you prefer but here is a brief overview of the ...
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1 vote

CRISPR screening and systems biology

What do you call screening results? Do you have a kind of array with protein or RNA data? If so, you can use several open-source tools available on the internet, like Enrichr or network analyst to ...
1 vote

CRISPR/Cas9 screen analysis with Mageck: paired-end sequencing

The other answer is incorrect. The original poster is asking about paired-end sequencing data, not paired treatment/control experimental design. Here is how you analyze paired-end sequencing data (...
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1 vote

How do I find the most similar sequences from a large set of short sequences?

I'm pretty sure that an all-vs-all approach is not feasible, but perhaps there's some trick that I'm missing. The "trick" is that I hadn't actually tried this, and Bowtie2 happens to be quite good at ...
  • 12k
1 vote

R packages for data analyses of pooled CRISPR screens

From my experience, there is few about CRISPR pooled screenings in R. One of them is ScreenBEAM. It uses a linear mixture model to determine significance at gene level by considering all the guides ...
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