broadinstitute/ABC-Enhancer-Gene-Prediction

Issues

• Where can i find the Reference files for the mouse Reference genome mm10

  #232 opened a month ago by mano2991
  0

• qnrom in config.yaml for different cells

  #231 opened a month ago by JasonLinjc
  1

• Quantile normalization

  #230 opened 2 months ago by engreitz
  0

• predict.py

  #228 opened 3 months ago by BERICP01
  0

• Install QC

  #211 opened 4 months ago by snglcl
  3

• Difference between EnhancerPredictionsFull_threshold0.02_self_promoter.tsv and EnhancerPredictions_threshold0.02_self_promoter.tsv

  #223 opened 4 months ago by NicoleYY77
  3

• Failure to replicate results

  #222 opened 4 months ago by PeterWang0502
  3

• Using our own file of promoters

  #218 opened 4 months ago by Kellydc15
  1

• can list of genes in the reference be the list of differential genes only?

  #212 opened 5 months ago by olechnwin
  3

• How to Recalculate ABC.Score Values for H3K27ac HiChIP + ATAC Data Analysis?

  #183 opened 5 months ago by Gemma-Zhang-326
  3

• Calculating ABC score using HiChIP and expression data

  #206 opened 5 months ago by anapkut
  2

• Input file

  #215 opened 5 months ago by shenlinyong
  1

• Apply ABC model to independent cell types

  #214 opened 5 months ago by NicoleYY77
  1

• Using ABC with .bedpe files

  #216 opened 5 months ago by MattQIMR
  0

• qnorm in config.yaml

  #192 opened 6 months ago by olechnwin
  11

• 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 opened 6 months ago by NicoleYY77
  6

• ABC with Hg38

  #197 opened 6 months ago by Sylviavictor
  3

• KeyError: 'ABC.Score'

  #193 opened 6 months ago by olechnwin
  4

• Documentation for outputs in Predictions folder

  #194 opened 6 months ago by olechnwin
  1

• gene expression input?

  #191 opened 6 months ago by olechnwin
  3

• EnhancerList.txt can be used as a normal enhancer list?

  #153 opened 6 months ago by wbszhu
  1

• chr9 Hi-C data

  #188 opened 6 months ago by TakuroIwami
  1

• key Errors of predicty.py

  #182 opened 8 months ago by tan5251
  2

• Use different chromatin assays to estimate enhancer activity

  #176 opened 8 months ago by nsamzhao
  1

• When I have experimental HiC data, should I predict with -scale_hic_using_powerlaw on?

  #181 opened 8 months ago by tan5251
  1

• About parameters to use when predicting with --scale_hic_using_powerlaw on

  #136 opened a year ago by aldenleung
  2

• load_hic_avg expects three columns, but the recommended average hic bed files have four columns

  #172 opened 9 months ago by pl92297
  4

• Refseq gene list

  #61 opened 3 years ago by yussufhajjaj
  3

• permissions error when cloning repository

  #175 opened 9 months ago by Philippa-W
  1

• difficulty reproducing the ABC score of K562's in Nature 2021

  #60 opened 9 months ago by mirahan
  4

• Downloading Hi-C Data for Chromosome 9

  #62 opened 9 months ago by ashvinravi
  3

• Refseq white list

  #63 opened 9 months ago by EnrichettaMileti
  3

• Is it possible to include HiC data for GRCh38?

  #64 opened 9 months ago by gaoyuanwang1976
  2

• juicebox_dump.py

  #65 opened 9 months ago by User-yx
  2

• How to make the average Hi-C profiles for hg38

  #67 opened 9 months ago by koh2ng0
  2

• Value error problem in the predict.py

  #68 opened 9 months ago by Samfouss
  1

• KeyError: 'end' with run.neighborhoods.py

  #70 opened 9 months ago by pgh10
  2

• Error: The requested genome file (None) could not be opened. Exiting!

  #82 opened 9 months ago by yizhang-zoey
  1

• Typos in README.md

  #141 opened 9 months ago by sassy-crick
  1

• Conda environment conflict

  #155 opened 9 months ago by maxdudek
  1

• gzip: stdout: Broken pipe

  #74 opened a year ago by wbszhu
  3

• EnhancerList and GeneList chromosomes must start with "chr"

  #76 opened a year ago by DustinSokolowski
  1

• Key errors of run.neighborhoods.py

  #114 opened a year ago by FatihSarigol
  2

• Function add_powerlaw_to_predictions in predictor.py uses incorrect arguments for function get_powerlaw_at_distance (dev branch)

  #108 opened a year ago by rosaxma
  0

• Issue with run.neighborhoods.py, "ValueError: You are trying to merge on object and float64 columns"

  #92 opened a year ago by LarkDamer
  0

• assert df.shape[0] == orig_shape, "Dimension mismatch"

  #73 opened a year ago by Andi964
  1

• SCALE normalization

  #75 opened a year ago by Andi964
  0

• promoter-promoter and enh-promoter interactions

  #72 opened 2 years ago by Abeer-hes
  0

• Is it possible for you to add .bigwig as inputfile format option for Quantifying Enhancer Activity?

  #71 opened 2 years ago by ezioljj
  0

• KeyError: 'ABC.Score' - predict.py fails to set the score column

  #69 opened 2 years ago by Bennibraun
  2