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biocore-ntnu
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epic
(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
31
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6
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Bam support
#44
endrebak
opened
7 years ago
2
Error calculating readlength
#43
abalter
closed
7 years ago
1
IndexError: list index out of range
#42
mnrusimh
closed
7 years ago
1
Improvements to file, tempdir, and command handling
#41
DarwinAwardWinner
closed
7 years ago
7
Google Groups
#40
c-guzman
closed
7 years ago
2
Temporary Directory
#39
c-guzman
closed
7 years ago
3
OverflowError: Cannot convert float infinity to integer
#38
c-guzman
closed
7 years ago
8
How to direct output to a file
#37
abhisheksinghnl
closed
6 years ago
2
EPIC stops if treatment and control are both input files
#36
c-guzman
closed
7 years ago
5
Usage with multiple treatments and controls
#35
ksiklenka
closed
7 years ago
2
Effective genome size for Rnor6
#34
abhisheksinghnl
closed
7 years ago
9
Bug in multiprocessing paired end data:
#33
endrebak
closed
6 years ago
3
Write something about epic not being suitable for single-chromosome files (yet, if ever)
#32
endrebak
closed
6 years ago
0
AssertionError: assert len(merged_df) == chip_df_nb_bins
#31
endrebak
closed
7 years ago
21
Multiprocessing exception at merging ChIP and Input
#30
balwierz
closed
7 years ago
5
Latest version of bioepic on anaconda is 0.0.6
#29
c-guzman
closed
7 years ago
4
Default parameters for gap
#28
Estel-Kitsune
closed
7 years ago
1
Add contribution guidelines
#27
endrebak
opened
8 years ago
0
OverflowError: cannot convert float infinity to integer
#26
Estel-Kitsune
closed
6 years ago
4
Make script to print system and library versions
#25
endrebak
closed
7 years ago
0
Using dm3 makes epic crash
#24
topalis
closed
7 years ago
5
Add cli option to list the genomes available?
#23
endrebak
opened
8 years ago
0
Add instructions how to add a new genome
#22
balwierz
closed
7 years ago
10
printmatrix not working for bepde
#21
endrebak
closed
7 years ago
1
Galaxy (usegalaxy.org) wrapper for epic
#20
mictadlo
closed
7 years ago
2
Write matrix of counts to file
#19
endrebak
closed
8 years ago
0
Add instructions on how to filter files in README.md
#18
endrebak
opened
8 years ago
0
Add file logger option
#17
endrebak
closed
6 years ago
0
Test that chip/input gives same result as chip/2*input
#16
endrebak
closed
8 years ago
1
Question about paired-end reads
#15
JFourquet
closed
8 years ago
3
Find readlength
#14
endrebak
closed
8 years ago
2
Remove debug info from log
#13
endrebak
opened
8 years ago
0
Automatically find appropriate effective genome size
#12
endrebak
closed
8 years ago
2
Bam test
#11
endrebak
closed
8 years ago
1
Fix p-value/FDR output
#10
endrebak
closed
8 years ago
0
Allow samtools filter flags + quality threshold on the command line?
#9
endrebak
closed
8 years ago
1
Add integration test that tests with bam file.
#8
endrebak
closed
8 years ago
0
configurable tempdir
#7
daler
closed
8 years ago
1
bedtools needs genome
#6
daler
closed
8 years ago
3
Create bigwig files for UCSC genome browser display?
#5
endrebak
closed
7 years ago
1
Paired-end read support
#4
mictadlo
closed
8 years ago
2
snakemake workflow for effective genome sizes
#3
daler
closed
8 years ago
14
Make it possible to enter fa/fai file on command line instead of genome
#2
mictadlo
closed
8 years ago
5
Epic-effective: Automatically remove bad chromos.
#1
endrebak
closed
8 years ago
1
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