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ArcInstitute
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ScreenPro2
Flexible analysis of high-content CRISPR screening
https://screenpro2.rtfd.io
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clarify references to elements in sgRNA library
#48
abearab
closed
7 months ago
0
mismatch allowance for sequence counting task
#47
abearab
opened
7 months ago
1
update `plotReplicateScatter` function
#46
abearab
closed
7 months ago
0
Question: library and sample format in cas9.py
#45
akshitasax
closed
7 months ago
6
major reformatting and introduce alpha version of CLI
#44
abearab
closed
7 months ago
1
Define `PooledScreens` and `GImaps` in assays module
#43
abearab
closed
7 months ago
0
Define `Counter` module for `fastq2count` tasks
#42
abearab
closed
7 months ago
0
Fix formatting for function comments
#41
abearab
closed
7 months ago
0
support cas12-screens
#40
abearab
closed
7 months ago
0
Process FASQ files for higher-order combinatorial perturbations
#39
abearab
closed
7 months ago
0
Improve NGS module
#38
abearab
closed
8 months ago
0
add features for processing single guide libraries
#37
abearab
closed
8 months ago
0
add draft fastq2counts functions for single-guide-design
#36
abearab
closed
8 months ago
1
Write CLI and draw step-by-step workflows
#35
abearab
closed
5 months ago
1
Reimplement `CRISPhieRmix` approch
#34
abearab
closed
8 months ago
0
Add z-score normalization option
#33
abearab
closed
9 months ago
1
Improve and fix `plotReplicateScatter` function
#32
abearab
closed
7 months ago
1
Add tutorials
#31
abearab
opened
10 months ago
0
Design relevant python objects
#30
abearab
closed
4 months ago
0
Create Issue forms
#29
abearab
closed
3 months ago
1
Design and implement `fastq2count` module
#28
abearab
closed
5 months ago
1
Include commonly used CRISPR library tables
#27
abearab
closed
9 months ago
0
Validating genome-scale guide RNA libraries
#26
abearab
closed
9 months ago
1
Split scripts for phenotype score calculation and statistical analysis
#25
abearab
closed
11 months ago
0
pytest fails without a clear reason
#24
abearab
closed
11 months ago
2
Run phenoScore on each samples pairs to get phenotypes per replicates.
#23
abearab
closed
11 months ago
0
Phenotype scatter plot for replicates as a QC analysis
#22
abearab
closed
11 months ago
0
Workflow for FACS-based screens
#21
abearab
closed
9 months ago
1
Workflow for survival screens
#20
abearab
closed
9 months ago
0
Define "population doublings" column for input sample sheet
#19
abearab
closed
11 months ago
0
Sort and find top `n` guide per target
#18
abearab
closed
3 months ago
0
Z-score normalization relative to negative control distribution
#17
abearab
closed
9 months ago
2
Find and filter out low counts in a pair-wise comparison
#16
abearab
closed
3 months ago
2
Support custom and common CRISPR libraries
#15
abearab
closed
8 months ago
1
Introduce `.pdata` matrix as part of assays objects
#14
abearab
closed
6 months ago
0
Implement workflows for common platforms and use cases
#13
abearab
closed
3 months ago
1
Implement methods for phenotype calculation and statistical analysis
#12
abearab
opened
11 months ago
1
Benjamini-Hochberg FDR calculation
#11
abearab
closed
8 months ago
1
Transparent methods for phenotype calculation and statistical analysis
#10
abearab
closed
7 months ago
0
Principal component analysis (PCA) of guide level phenotypes
#9
abearab
closed
7 months ago
0
Improve documentations
#8
abearab
closed
3 months ago
0
Add a section for background and references
#7
abearab
opened
11 months ago
1
Reword oligo to avoid confusion
#6
abearab
closed
7 months ago
0
Include citation(s)
#5
abearab
closed
7 months ago
1
Gold standard AUC/ROC hit comparison across pipelines
#4
abearab
closed
3 months ago
3
Provide example with a toy dataset
#3
abearab
closed
3 months ago
0
Define I/O for common CRISPR library platforms
#2
abearab
closed
7 months ago
0
Code and knowledge transfer from GilbertLabUCSF repository and issues
#1
abearab
closed
11 months ago
1
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