Ecosyste.ms: Issues

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GitHub / ay-lab/fithic issues and pull requests

#69 - "util" scripts missing from conda install

Issue - State: open - Opened by vidal-adrien 9 months ago - 1 comment

#67 - Questions about using .hic as input

Issue - State: open - Opened by nyuhic over 1 year ago

#66 - Out of range

Issue - State: open - Opened by Lucas446 over 1 year ago - 8 comments

#65 - fithic "invalid syntax"

Issue - State: open - Opened by Lucas446 over 1 year ago - 1 comment

#64 - Does fithic work on single chromosome inputs?

Issue - State: open - Opened by Jakob-Zerbs over 1 year ago

#63 - install problem

Issue - State: open - Opened by jiangshan529 about 2 years ago - 6 comments

#62 - Update code

Pull Request - State: closed - Opened by souryacs over 2 years ago

#61 - Update README.md

Pull Request - State: closed - Opened by souryacs over 2 years ago

#60 - FitHiC2 with replicates

Issue - State: closed - Opened by DaianeH over 2 years ago

#59 - fragmentMid

Issue - State: closed - Opened by BenxiaHu over 2 years ago - 1 comment

#58 - Any example of using .hic file as the input?

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

#57 - merge_filter reduces significant interactions from 12M to 10k

Issue - State: open - Opened by pna059 over 2 years ago

#56 - Out of 70041 loci 70041 were discarded with biases not in range [0.5 2]

Issue - State: open - Opened by nisar-BIGPM over 2 years ago - 3 comments

#55 - Difference between ICE and KR biases. Setting up the bias limits.

Issue - State: open - Opened by pna059 over 2 years ago - 5 comments

#54 - list index out of range

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

#53 - how to prepare my `input file`?

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

#52 - test run AttributeError

Issue - State: closed - Opened by mannekim over 2 years ago - 1 comment

#51 - HiCKRy.py KeyError: '0'

Issue - State: closed - Opened by mannekim over 2 years ago - 5 comments

#50 - Allele chromatin loop

Issue - State: open - Opened by BenxiaHu over 2 years ago

#49 - error while running fithic with data generated by hic-pro

Issue - State: closed - Opened by LinXialab about 3 years ago - 8 comments

#48 - Fragment length is not consistent with fithic resolution (-r) in tests data

Issue - State: open - Opened by bnjvrjnke about 3 years ago - 1 comment

#47 - sequencing depth for loops

Issue - State: open - Opened by BenxiaHu about 3 years ago - 6 comments

#46 - fithic crash

Issue - State: open - Opened by fgualdr over 3 years ago - 1 comment

#45 - HiCKRy.py generated extreme bias value

Issue - State: open - Opened by QianzhaoJ over 3 years ago - 1 comment

#44 - Missing chr1 in output

Issue - State: closed - Opened by GRGong over 3 years ago - 1 comment

#43 - FitHic crashes

Issue - State: open - Opened by joachimwolff over 3 years ago - 1 comment

#42 - TypeError: can only concatenate str (not "int") to str

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

#41 - HiCKRy.py Key errors

Issue - State: open - Opened by Jssmith91 over 3 years ago - 8 comments

#40 - How to decide the bin size in interaction loops?

Issue - State: open - Opened by shanwai1234 over 3 years ago - 2 comments

#39 - ValueError: max() arg is an empty sequence

Issue - State: closed - Opened by sunthink almost 4 years ago - 3 comments

#38 - error while running FitHiC

Issue - State: open - Opened by priyatamapandey almost 4 years ago - 29 comments

#37 - OverflowError: cannot convert float infinity to integer

Issue - State: closed - Opened by HappyLife-together almost 4 years ago - 1 comment

#36 - OverflowError: cannot convert float infinity to integer

Issue - State: open - Opened by smurthy55 almost 4 years ago - 3 comments

#34 - Generate biasfile/KRnorm vector

Issue - State: closed - Opened by gheger11 about 4 years ago - 1 comment

#33 - Fit-Hic error

Issue - State: closed - Opened by BenxiaHu about 4 years ago

#32 - Running error

Issue - State: closed - Opened by JhinAir about 4 years ago - 7 comments

#31 - q-value is always 1 when running FitHiC2 using allValidPairs input

Issue - State: open - Opened by smurthy55 over 4 years ago - 1 comment

#30 - Question about the output of merge-filter.sh

Issue - State: closed - Opened by QianzhaoJ over 4 years ago

#29 - Can't Open File

Issue - State: closed - Opened by aakashsur over 4 years ago - 1 comment

#28 - Standard Error is always 0

Issue - State: closed - Opened by joreynajr over 4 years ago - 4 comments

#27 - Merge filter generalizable?

Issue - State: closed - Opened by jessakay over 4 years ago - 1 comment

#26 - Advice on converting pairix or cooler format to fithic format

Issue - State: closed - Opened by cjy8709 almost 5 years ago - 2 comments

#25 - error while using fithic for the interchromosomal interactions

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

#24 - Can fithic run low resolution HiC data？

Issue - State: closed - Opened by Antony-1996 over 5 years ago - 2 comments

#23 - Where to find fragments argument from HiC Pro Pipeline?

Issue - State: closed - Opened by emarti88 over 5 years ago - 1 comment

#22 - fixed a bug when there are empty chromosomes when reading fragments.

Pull Request - State: closed - Opened by ningbioinfo over 5 years ago - 4 comments

#21 - Minor bug when testing installation

Issue - State: closed - Opened by kalavattam over 5 years ago - 2 comments

#20 - Illegal fragment pair

Issue - State: closed - Opened by RuiqinZheng almost 6 years ago - 4 comments

#19 - 2.0.6

Pull Request - State: closed - Opened by aryakaul almost 6 years ago

#18 - How to get different contacts?

Issue - State: closed - Opened by liufuyan2016 about 6 years ago - 1 comment

#17 - fix html bug

Pull Request - State: closed - Opened by aryakaul about 6 years ago

#16 - HTML file has broken links to FitHiC outputs

Issue - State: closed - Opened by ckmah about 6 years ago - 3 comments

#15 - another bug during bias parsing

Pull Request - State: closed - Opened by gongyh about 6 years ago - 1 comment

#14 - fix a bug in read_biases

Pull Request - State: closed - Opened by gongyh about 6 years ago

#13 - intra vs inter chromosomal counts in input

Issue - State: closed - Opened by armenabnousi about 6 years ago - 2 comments

#12 - Update README.md

Pull Request - State: closed - Opened by ay-lab about 6 years ago

#11 - Development

Pull Request - State: closed - Opened by ghost over 6 years ago

#10 - Development

Pull Request - State: closed - Opened by aryakaul over 6 years ago

#9 - TypeError: coercing to Unicode: need string or buffer, NoneType found

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

#8 - --visual flag has cutoff images

Issue - State: closed - Opened by aakashsur almost 7 years ago - 5 comments

#7 - Enhancement: Check whether gzipped or not for input files.

Issue - State: closed - Opened by aakashsur almost 7 years ago - 1 comment

#6 - Matplotlib Backend Error

Issue - State: closed - Opened by aakashsur almost 7 years ago - 1 comment

#5 - fithic run error

Issue - State: closed - Opened by liufuyan2016 almost 7 years ago - 2 comments

#4 - FitHiC run error

Issue - State: closed - Opened by garentian almost 7 years ago - 5 comments

#3 - Scikit-learn broken command

Issue - State: closed - Opened by aakashsur almost 7 years ago - 1 comment

#2 - Update Readme

Issue - State: closed - Opened by aakashsur almost 7 years ago - 1 comment

#1 - Added files via upload

Pull Request - State: closed - Opened by ay-lab over 8 years ago