perslab CELLECT issues - Githubissues

perslab / CELLECT

CELLECT (CELL-type Expression-specific integration for Complex Traits)

GNU General Public License v3.0

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No SNP rsID column in GWAS dataset

#46 AnjaMJ closed 4 years ago
2
Check expression specificity annotation names (ES header)

#45 DaianeH opened 4 years ago
26
System python being called within conda environment

#44 Tobi1kenobi opened 4 years ago
0
Error in rule compute_LD_scores:

#43 willrosenow closed 4 years ago
6
Does not work with precomputed MOCA data

#42 lamdan2 closed 4 years ago
3
explicit error when CELLEX input does not contain human Ensembl gene IDs

#41 pascaltimshel opened 4 years ago
0
Explicit failure when no genes found

#40 pvtodorov opened 4 years ago
0
Error in rule parse_results

#39 vgastaldi closed 4 years ago
2
Restructured CELLECT-LDSC for continuous annotations

#38 Tobi1kenobi closed 4 years ago
0
updated documentation

#37 pvtodorov closed 4 years ago
1
CELLECT LDSC Tutorial produces numpy import error

#36 pvtodorov closed 4 years ago
4
CELLECT fails to run with any provided yml

#35 pvtodorov closed 4 years ago
3
conditional analysis does work with multiple expression specificity datasets

#34 pascaltimshel opened 4 years ago
0
config file: add support for annotation regex/globbing [annotations: "*"]

#33 pascaltimshel opened 5 years ago
2
munge_sumstats.py / mtag_munge.py hanging

#32 liubovpashkova closed 4 years ago
1
make_multigenesets_snake.py will generate undesired results if the file is seperated by other seperators than ','

#31 bengnielsen closed 5 years ago
1
development branch: Error in rule compute_LD_scores

#30 JonThom closed 5 years ago
2
Develop

#29 Tobi1kenobi closed 5 years ago
0
python3: can't open file 'scripts/parse_results_cmdline.py': [Errno 2] No such file or directory

#28 JonThom closed 5 years ago
2
ModuleNotFoundError: No module named 'datrie'

#27 JonThom closed 5 years ago
2
Write test routines (e.g. check correct Git LFS cloning)

#26 pascaltimshel opened 5 years ago
0
AmbiguousRuleException: Rules 10 and 9 are ambiguous

#25 pascaltimshel closed 5 years ago
12
_get_label_or_level_values KeyError: 'GENE'

#24 JonThom closed 5 years ago
2
Lack of automated testing

#23 Tobi1kenobi opened 5 years ago
0
Generation of multigenesets/accept multigeneset as input

#22 Tobi1kenobi closed 4 years ago
1
Integrate munging of GWAS summary stats

#21 Tobi1kenobi opened 5 years ago
0
LD-based windows SNP loss

#20 Tobi1kenobi closed 4 years ago
0
speed-up build DAG by optimizing CELLECT-LDSC snakefile

#19 pascaltimshel closed 5 years ago
1
add config file validation

#18 pascaltimshel opened 5 years ago
0
check that annotation names are 'clean'

#17 pascaltimshel closed 5 years ago
0
Use snakemake temp() function to minimize storage

#16 pascaltimshel closed 5 years ago
2
Better utilise the dictionaries in the config.yml

#15 Tobi1kenobi closed 5 years ago
1
Clean snakefile for dependency on pandas/numpy

#14 pascaltimshel closed 5 years ago
0
Implement logger / handle printing

#13 pascaltimshel closed 5 years ago
0
Prune conda envs dependencies

#12 pascaltimshel closed 5 years ago
1
Add support for matrix specificity input [MAGMA support]

#11 pascaltimshel closed 5 years ago
0
Check for double underscores (__) in GWAS file names / GWAS ID names

#10 pascaltimshel closed 5 years ago
1
Add (error) check for too small annotations: S-LDSC

#9 pascaltimshel opened 5 years ago
0
Bedtools merge is not appropriate for continuous data

#8 Tobi1kenobi closed 4 years ago
3
Implement h2 analysis

#7 Tobi1kenobi closed 5 years ago
1
multigeneset file has to contain CELLEX output data from multiple datasets

#6 Tobi1kenobi closed 5 years ago
1
run_prefix in snakemake doesn't cover parameter changes

#5 Tobi1kenobi closed 5 years ago
0
Make_all_genes script can only run once

#4 Tobi1kenobi closed 5 years ago
0
Crashes if 'nan' is a celltype in the multigeneset

#3 Tobi1kenobi opened 5 years ago
0
Implement conditional analysis

#2 Tobi1kenobi closed 5 years ago
0
Control.all_genes_in_dataset should be generated by snakemake

#1 Tobi1kenobi closed 5 years ago
0