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keoughkath
/
AlleleAnalyzer
A software tool for personalized and allele-specific CRISPR editing.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1783-3
MIT License
16
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5
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bcftools version
#50
reubenthomas
opened
1 year ago
2
Error designing allele-specific guides
#49
reubenthomas
closed
1 year ago
3
sample bcf files
#48
BingbingYuan
closed
1 year ago
1
SaCas9-KKH variant PAM
#47
keoughkath
closed
5 years ago
1
Mpo crispor work
#46
allgenesconsidered
closed
6 years ago
1
gen_sgRNAs --bed option redundant
#45
keoughkath
closed
5 years ago
0
Altered the set cover optimization to take long format input
#44
slyalina
closed
6 years ago
0
Mpo issues 37 39
#43
allgenesconsidered
closed
6 years ago
1
Fixed gens not working with single locus hg38 samples.
#42
allgenesconsidered
closed
6 years ago
0
BUGFIX: Filter out N now works with multi-cas files, changes to plotting asthetics in make_pretty_igv
#41
allgenesconsidered
closed
6 years ago
1
Rework of annot_variants. Works with single or multi-locus gens files.
#40
allgenesconsidered
closed
6 years ago
1
Suggestion: Add metadata to hdf5 files.
#39
allgenesconsidered
closed
6 years ago
1
annot_variants.py unable to parse multi-locus gens files.
#38
allgenesconsidered
closed
6 years ago
0
Output naming consistency (whether to include a discriptive suffix or not).
#37
allgenesconsidered
closed
6 years ago
1
Extra 'chr' in 5' PAMs
#36
allgenesconsidered
closed
6 years ago
0
Edits to gen_sgRNA, filter for N variants and RNA seq
#35
allgenesconsidered
closed
6 years ago
0
N position in Pam filter
#34
keoughkath
closed
6 years ago
2
RNA seq for gen sgRNA
#33
keoughkath
closed
6 years ago
1
Mpo annotate variants
#32
allgenesconsidered
closed
6 years ago
1
Updated README with wiki changes.
#31
allgenesconsidered
closed
6 years ago
0
Update get_gens_df.py
#30
allgenesconsidered
closed
6 years ago
1
CRISPOR with non-spCas9
#29
keoughkath
closed
5 years ago
0
implement new Cas feature in pam_pos scripts (preprocessing)
#28
keoughkath
closed
6 years ago
2
Mpo multi locus test
#27
allgenesconsidered
closed
6 years ago
0
Hotfixes to gen_sgRNAs.py, typos in code.
#26
allgenesconsidered
closed
6 years ago
0
eliminate dependence on crisprtools
#25
keoughkath
closed
6 years ago
0
implement strict option in gen_sgRNAs
#24
keoughkath
closed
6 years ago
1
integrate new CAS_LIST feature into gen_targ_dfs script
#23
keoughkath
closed
6 years ago
1
naming inconsistencies
#22
keoughkath
closed
6 years ago
0
Mpo gen sgrnas edit
#21
allgenesconsidered
closed
6 years ago
0
Mpo get chr tab hotfix
#20
allgenesconsidered
closed
6 years ago
0
Abstracting sgRNA generation functions, added additional checks for hdf files.
#19
allgenesconsidered
closed
6 years ago
1
irregularities between file naming for targ and gen file generation
#18
keoughkath
closed
6 years ago
1
Added rsID notation for NaN variants.
#17
allgenesconsidered
closed
6 years ago
0
Fixed pd.concat call in wrong spot.
#16
allgenesconsidered
closed
6 years ago
0
multiplexing and homozygous sgRNAs
#15
keoughkath
closed
6 years ago
0
Issues with conda environment in gen_sgRNAs.py
#14
allgenesconsidered
closed
6 years ago
2
Mpo reverse complement
#13
allgenesconsidered
closed
6 years ago
0
Fixed issues with make_pretty_igv.py not running. Also added HET chec…
#12
allgenesconsidered
closed
6 years ago
1
Update make_pretty_igv.py
#11
allgenesconsidered
closed
6 years ago
1
Update gen_targ_dfs.py
#10
allgenesconsidered
closed
6 years ago
1
Small change to get_chr_table, made complete python version.
#9
allgenesconsidered
closed
6 years ago
2
Small change to get_chr_table, made complete python version.
#8
allgenesconsidered
closed
6 years ago
0
Fix gen sgrnas
#7
keoughkath
closed
6 years ago
0
Mpo edit wiki
#6
allgenesconsidered
closed
6 years ago
1
Allgenesconsidered mpo test
#5
keoughkath
closed
6 years ago
0
Added "skinny" and "thick" blocks to the output of make_pretty_igv.py…
#4
allgenesconsidered
closed
6 years ago
1
Additional changes to get_chr_tables.sh, CONFIRMED working with multisample vcf!
#3
allgenesconsidered
closed
6 years ago
1
Create LICENSE
#2
keoughkath
closed
6 years ago
0
Edited get_chr_tables to check bcltools version and to use PATH
#1
allgenesconsidered
closed
6 years ago
0
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