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broadinstitute
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ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
MIT License
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--hic_gamma and --hic_scale parameter for ENCFF621AIY.hic
#239
L1angyan
opened
1 month ago
1
Can not make the juice dump HiC data for chr9 on K562_combined_30.hic with resolution lower than 25000
#238
nttg8100
opened
2 months ago
0
New pipeline v1.1.2 ABC failed to use the ABC for hg19 on K562 dataset
#237
nttg8100
closed
2 months ago
0
silencer
#236
tan5251
opened
2 months ago
0
Duplicate score_column in `predict.py`
#235
nttg8100
opened
2 months ago
1
How to specify more than 2 DHS replication ?
#234
nttg8100
closed
2 months ago
1
Where I can get the qnorm file
#233
nttg8100
closed
2 months ago
1
Where can i find the Reference files for the mouse Reference genome mm10
#232
mano2991
opened
3 months ago
0
qnrom in config.yaml for different cells
#231
JasonLinjc
opened
3 months ago
1
Quantile normalization
#230
engreitz
opened
4 months ago
0
Update utils.smk
#229
mayasheth
closed
4 months ago
0
predict.py
#228
BERICP01
opened
4 months ago
0
Update README.md
#227
atancoder
closed
5 months ago
0
Dev
#226
atancoder
closed
5 months ago
0
Update circleci config.yml
#225
atancoder
closed
5 months ago
0
utilize amazon link as the encode link leads to a segfault in CircleCI
#224
atancoder
closed
5 months ago
0
Difference between EnhancerPredictionsFull_threshold0.02_self_promoter.tsv and EnhancerPredictions_threshold0.02_self_promoter.tsv
#223
NicoleYY77
opened
6 months ago
3
Failure to replicate results
#222
PeterWang0502
closed
5 months ago
3
clean up hic processing code
#221
atancoder
closed
6 months ago
0
update bedpe file creation
#220
atancoder
closed
6 months ago
0
update bedpe file format
#219
atancoder
closed
6 months ago
0
Using our own file of promoters
#218
Kellydc15
closed
6 months ago
1
update troubleshooting doc
#217
atancoder
closed
6 months ago
0
Using ABC with .bedpe files
#216
MattQIMR
closed
6 months ago
0
Input file
#215
shenlinyong
closed
6 months ago
1
Apply ABC model to independent cell types
#214
NicoleYY77
closed
6 months ago
1
update docs w/ troubleshooting. update release.yml
#213
atancoder
closed
7 months ago
0
can list of genes in the reference be the list of differential genes only?
#212
olechnwin
closed
6 months ago
3
Install QC
#211
snglcl
closed
5 months ago
3
Dev
#210
atancoder
closed
7 months ago
0
prepare for main merge
#209
atancoder
closed
7 months ago
0
increase output timeout for circleci
#208
atancoder
closed
7 months ago
0
ValueError("Error counting BAM file: count <= 0") ValueError: Error counting BAM file: count <= 0 when trying to replicate the ABC score results of K562
#207
NicoleYY77
closed
7 months ago
6
Calculating ABC score using HiChIP and expression data
#206
anapkut
closed
6 months ago
2
Update from main
#205
atancoder
closed
8 months ago
0
use distributed pytest
#204
atancoder
closed
8 months ago
0
fix 1 of the tests to use powerlaw to improve memory consumption
#203
atancoder
closed
8 months ago
0
Change some prediction column names of ABC
#202
atancoder
closed
8 months ago
1
Fix qnorm
#201
atancoder
closed
8 months ago
0
Main merge
#200
atancoder
closed
8 months ago
0
Fix issue with smartopen dependency and snakemake
#199
atancoder
closed
8 months ago
0
Merge dev to main
#198
atancoder
closed
8 months ago
0
ABC with Hg38
#197
Sylviavictor
closed
8 months ago
3
support choosing the pre-set ABC threshold based on inputs
#196
atancoder
closed
8 months ago
0
Better pl support
#195
atancoder
closed
8 months ago
0
Documentation for outputs in Predictions folder
#194
olechnwin
closed
8 months ago
1
KeyError: 'ABC.Score'
#193
olechnwin
closed
8 months ago
4
qnorm in config.yaml
#192
olechnwin
closed
8 months ago
11
gene expression input?
#191
olechnwin
closed
8 months ago
3
Catlas run
#190
atancoder
closed
8 months ago
0
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