biocore-ntnu/epic issues and pull requests

#94 - Arabidopsis thaliana

Issue - State: open - Opened by mtrejo96 over 4 years ago - 2 comments

#93 - ChIP-seq WT vs mutants comparison

Issue - State: open - Opened by nermah1 over 4 years ago - 2 comments

#92 - Genomes cannot find

Issue - State: open - Opened by tan5251 over 4 years ago

#91 - Epic-effective: TypeError: cannot concatenate 'str' and 'NoneType' objects

Issue - State: open - Opened by aboyd003 over 5 years ago - 5 comments

#90 - Epic depricated

Issue - State: open - Opened by parida007 almost 7 years ago - 1 comment

#89 - Stop coveralls from being picked up as a dependency

Pull Request - State: closed - Opened by rmsds almost 7 years ago - 5 comments

#88 - How does EPIC work ?

Issue - State: open - Opened by nservant almost 7 years ago - 6 comments

#87 - Epic effective for

Issue - State: open - Opened by parida007 almost 7 years ago - 11 comments

#86 - calculating memory requirements based on bam file size

Issue - State: open - Opened by avilella about 7 years ago - 7 comments

#85 - are read ids necessary in SE mode?

Issue - State: closed - Opened by avilella about 7 years ago - 1 comment

#84 - conda still installs 0.2.9

Issue - State: closed - Opened by avilella about 7 years ago - 10 comments

#83 - cannot recognize genome

Issue - State: open - Opened by Wangcn81 about 7 years ago - 5 comments

#82 - problem with output

Issue - State: closed - Opened by lucacozzuto about 7 years ago - 10 comments

#81 - trackline and recommanded parameters

Issue - State: open - Opened by nservant about 7 years ago - 9 comments

#80 - epic and conda

Issue - State: closed - Opened by nservant about 7 years ago - 2 comments

#79 - epic-merge throws an error of ValueError: Cannot convert NA to integer

Issue - State: closed - Opened by lucacozzuto about 7 years ago - 3 comments

#78 - Best choice parameters

Issue - State: open - Opened by JoseCorCab over 7 years ago - 1 comment

#77 - run epic without control samples

Issue - State: closed - Opened by james-chuang over 7 years ago - 2 comments

#76 - salmo salar genome request

Issue - State: open - Opened by etarisal over 7 years ago - 11 comments

#75 - Repair effective_sizes/dm6_50.txt

Pull Request - State: closed - Opened by palmercd over 7 years ago - 2 comments

#74 - epic 0.2.9 compute_score_threshold.py:24 RuntimeWarning: divide by zero encountered in log

Issue - State: open - Opened by grendon over 7 years ago - 6 comments

#73 - No Releases

Issue - State: open - Opened by dslater82 over 7 years ago - 2 comments

#72 - Recommend publication

Issue - State: open - Opened by Bohdan-Khomtchouk over 7 years ago - 1 comment

#71 - epicR?

Issue - State: open - Opened by Bohdan-Khomtchouk over 7 years ago - 5 comments

#70 - where "chr1_before_find_islands.csv" file comes from?

Issue - State: closed - Opened by zhenyisong over 7 years ago - 2 comments

#69 - Create bigwigs in epic-cluster

Issue - State: open - Opened by endrebak over 7 years ago
Labels: in progress

#68 - Add C. elegans genome?

Issue - State: open - Opened by teresawlee over 7 years ago - 3 comments
Labels: in progress

#67 - epic - bed formats

Issue - State: closed - Opened by sejmodha almost 8 years ago - 2 comments

#66 - epic-merge fails to run

Issue - State: closed - Opened by nw11 almost 8 years ago - 4 comments

#65 - Genome request

Issue - State: closed - Opened by sejmodha almost 8 years ago - 4 comments

#64 - cat: write error: Broken pipe

Issue - State: closed - Opened by romanhaa almost 8 years ago - 7 comments

#63 - -w parameter

Issue - State: closed - Opened by yeroslaviz about 8 years ago - 7 comments

#62 - Can we run Epic without a control file?

Issue - State: closed - Opened by CodeInTheSkies about 8 years ago - 2 comments

#61 - i2bw correction in the doc

Issue - State: closed - Opened by yeroslaviz about 8 years ago - 1 comment

#60 - bigwig parameter with epic

Issue - State: closed - Opened by yeroslaviz about 8 years ago - 6 comments

#59 - adding saccer3 to the genome list

Issue - State: closed - Opened by yeroslaviz about 8 years ago - 7 comments

#58 - total_genome_length is not defined

Issue - State: closed - Opened by yeroslaviz about 8 years ago - 1 comment

#57 - OverflowError for paired-end reads bedpe files

Issue - State: closed - Opened by yeroslaviz about 8 years ago - 20 comments

#56 - Score & Fold_change? What do they mean and how to caculate them?

Issue - State: open - Opened by zhenyisong about 8 years ago - 1 comment

#55 - Concating dfs pandas error

Issue - State: closed - Opened by saycheeeeese over 8 years ago - 2 comments

#54 - custom chromosomes with . in name

Issue - State: closed - Opened by saycheeeeese over 8 years ago - 5 comments

#53 - Use unique filenames for --sum-bigwig option

Issue - State: closed - Opened by quantumdot over 8 years ago - 2 comments

#52 - Clarify Read Inputs and Differential Peak Calling

Issue - State: open - Opened by quantumdot over 8 years ago - 1 comment

#51 - Effective Genome Size

Issue - State: closed - Opened by c-guzman over 8 years ago - 2 comments

#50 - epic-effective cannot find jellyfish

Issue - State: open - Opened by IanCodes over 8 years ago - 3 comments

#49 - Andaconda Update

Issue - State: closed - Opened by c-guzman over 8 years ago - 6 comments

#48 - -k FLAG

Issue - State: closed - Opened by c-guzman over 8 years ago - 2 comments

#47 - Add type annotations for all functions

Pull Request - State: closed - Opened by DarwinAwardWinner almost 9 years ago - 6 comments

#46 - epic - is it usual that analyses take time?

Issue - State: closed - Opened by anishdattani almost 9 years ago - 12 comments

#45 - bioepic: OverflowError: cannot convert float infinity to integer

Issue - State: open - Opened by anishdattani almost 9 years ago - 4 comments

#44 - Bam support

Issue - State: open - Opened by endrebak almost 9 years ago - 2 comments

#43 - Error calculating readlength

Issue - State: closed - Opened by abalter almost 9 years ago - 1 comment

#42 - IndexError: list index out of range

Issue - State: closed - Opened by mnrusimh almost 9 years ago - 1 comment

#41 - Improvements to file, tempdir, and command handling

Pull Request - State: closed - Opened by DarwinAwardWinner almost 9 years ago - 7 comments

#40 - Google Groups

Issue - State: closed - Opened by c-guzman almost 9 years ago - 2 comments

#39 - Temporary Directory

Issue - State: closed - Opened by c-guzman almost 9 years ago - 3 comments

#38 - OverflowError: Cannot convert float infinity to integer

Issue - State: closed - Opened by c-guzman almost 9 years ago - 8 comments

#37 - How to direct output to a file

Issue - State: closed - Opened by abhisheksinghnl about 9 years ago - 2 comments

#36 - EPIC stops if treatment and control are both input files

Issue - State: closed - Opened by c-guzman about 9 years ago - 5 comments

#35 - Usage with multiple treatments and controls

Issue - State: closed - Opened by ksiklenka about 9 years ago - 2 comments

#34 - Effective genome size for Rnor6

Issue - State: closed - Opened by abhisheksinghnl about 9 years ago - 9 comments

#33 - Bug in multiprocessing paired end data:

Issue - State: closed - Opened by endrebak about 9 years ago - 3 comments

#32 - Write something about epic not being suitable for single-chromosome files (yet, if ever)

Issue - State: closed - Opened by endrebak about 9 years ago

#31 - AssertionError: assert len(merged_df) == chip_df_nb_bins

Issue - State: closed - Opened by endrebak about 9 years ago - 21 comments

#30 - Multiprocessing exception at merging ChIP and Input

Issue - State: closed - Opened by balwierz about 9 years ago - 5 comments

#29 - Latest version of bioepic on anaconda is 0.0.6

Issue - State: closed - Opened by c-guzman about 9 years ago - 4 comments

#28 - Default parameters for gap

Issue - State: closed - Opened by Estel-Kitsune about 9 years ago - 1 comment

#27 - Add contribution guidelines

Issue - State: open - Opened by endrebak about 9 years ago

#26 - OverflowError: cannot convert float infinity to integer

Issue - State: closed - Opened by Estel-Kitsune about 9 years ago - 4 comments

#25 - Make script to print system and library versions

Issue - State: closed - Opened by endrebak about 9 years ago

#24 - Using dm3 makes epic crash

Issue - State: closed - Opened by topalis about 9 years ago - 5 comments

#23 - Add cli option to list the genomes available?

Issue - State: open - Opened by endrebak about 9 years ago

#22 - Add instructions how to add a new genome

Issue - State: closed - Opened by balwierz about 9 years ago - 10 comments

#21 - printmatrix not working for bepde

Issue - State: closed - Opened by endrebak about 9 years ago - 1 comment
Labels: bug

#20 - Galaxy (usegalaxy.org) wrapper for epic

Issue - State: closed - Opened by mictadlo about 9 years ago - 2 comments

#19 - Write matrix of counts to file

Issue - State: closed - Opened by endrebak about 9 years ago

#18 - Add instructions on how to filter files in README.md

Issue - State: open - Opened by endrebak about 9 years ago

#17 - Add file logger option

Issue - State: closed - Opened by endrebak about 9 years ago

#16 - Test that chip/input gives same result as chip/2*input

Issue - State: closed - Opened by endrebak about 9 years ago - 1 comment

#15 - Question about paired-end reads

Issue - State: closed - Opened by JFourquet over 9 years ago - 3 comments

#14 - Find readlength

Pull Request - State: closed - Opened by endrebak over 9 years ago - 2 comments

#13 - Remove debug info from log

Issue - State: open - Opened by endrebak over 9 years ago

#12 - Automatically find appropriate effective genome size

Issue - State: closed - Opened by endrebak over 9 years ago - 2 comments
Labels: enhancement

#11 - Bam test

Pull Request - State: closed - Opened by endrebak over 9 years ago - 1 comment

#10 - Fix p-value/FDR output

Issue - State: closed - Opened by endrebak over 9 years ago
Labels: bug

#9 - Allow samtools filter flags + quality threshold on the command line?

Issue - State: closed - Opened by endrebak over 9 years ago - 1 comment

#8 - Add integration test that tests with bam file.

Issue - State: closed - Opened by endrebak over 9 years ago

#7 - configurable tempdir

Pull Request - State: closed - Opened by daler over 9 years ago - 1 comment

#6 - bedtools needs genome

Issue - State: closed - Opened by daler over 9 years ago - 3 comments
Labels: bug

#5 - Create bigwig files for UCSC genome browser display?

Issue - State: closed - Opened by endrebak over 9 years ago - 1 comment

#4 - Paired-end read support

Issue - State: closed - Opened by mictadlo over 9 years ago - 2 comments
Labels: enhancement

#3 - snakemake workflow for effective genome sizes

Pull Request - State: closed - Opened by daler over 9 years ago - 14 comments

#2 - Make it possible to enter fa/fai file on command line instead of genome

Issue - State: closed - Opened by mictadlo over 9 years ago - 5 comments
Labels: enhancement

#1 - Epic-effective: Automatically remove bad chromos.

Issue - State: closed - Opened by endrebak over 9 years ago - 1 comment
Labels: enhancement

GitHub / biocore-ntnu/epic issues and pull requests