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This issue covers 3 different types of CRISPR screens.
Related publications:
* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8443183/
* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181115/
* htt…
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I was playing around with the `crispr` module and came across a weird error where the cut coordinates of a `cas9` object were way larger than the target sequence.
```
from pydna.dseqrecord import …
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For Crispr off target effects we need to do the variant calling for each sample to the parental cell line. I would propose to encode this in the units:
patient_id = parental cell line
sample = nor…
votti updated
2 months ago
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Are you adding any features for CRISPR-Csm transcript targeting systems?
https://www.nature.com/articles/s41587-022-01649-9
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Hello, I'm new to bioinformatics and I'm trying to run this command using your program
_design.py complete-targets fasta /nfs7/BPP/Chang_Lab/buchanri/agro_crispr_dx/data/fna_assemblies/B133-95_BV2_…
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Hello,
I am running your tool from the command line using the following command:
perl RD-build.pl -m cas9 -i /data/genome.fa -g /data/genome_annotation.gff -o /data/sgRNA/genomes -l crispr_test -U…
nllg updated
12 months ago
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**Analysis of tested guide RNA’s used for gene editing via CRISPR to predict optimal future guide sequences**
Despite the apparent simplicity of this sequence matching strategy to target the CRISPR…
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Hey everyone, we're trying to compare data across "perturbation-universes". For this, we're having a deeper look into the controls in the CRISPR plates.
Their layout is, for example, like this:
![…
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- [ ] #4
**`phenoscore`**
- [x] #25
- [ ] Implement ScreenProcessing's stats for libraries with multiple sgRNA elements per target
- [ ] #71
- [ ] Write function to run robust ranking aggregat…
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Hello!
I just had a quick question. Looking through the documentation I am a little unclear if knock-knock can be used to analyze CRISPR NGS data generated using multiplexed PCR (e.g. multiple ampl…