aryeelab/hichipper issues and pull requests

#96 - Unable to install hichipper

Issue - State: open - Opened by madetunj 13 days ago

#95 - Conceptual question: identifying anchors

Issue - State: open - Opened by evaham1 over 1 year ago

#94 - userSuppliedPeaks.bed.tmp_pad.bed.tmprf.tmp

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

#93 - Rscript path

Issue - State: open - Opened by yanchunzhang about 2 years ago

#92 - "error in evaluating the argument 'object' in selecting a method for function 'summary': missing value where TRUE/FALSE needed"

Issue - State: open - Opened by Moonriver1988 almost 3 years ago - 3 comments

#91 - Something went wrong in determining peaks for anchor inference; rerun with the flag to debug.

Issue - State: open - Opened by Gemma-Zhang-326 about 3 years ago - 4 comments

#90 - problem with python script

Issue - State: open - Opened by robeach78 over 3 years ago - 3 comments

#89 - Error determining peaks for anchor inference

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

#88 - Something went wrong in determining peaks for anchor inference

Issue - State: open - Opened by woshiyangsi almost 4 years ago

#87 - Question about summary table in QC report HTML page

Issue - State: open - Opened by ledsall almost 4 years ago

#86 - error in running qcReport_make.Rmd

Issue - State: open - Opened by jielv about 4 years ago - 1 comment

#85 - "*_temporary_hichipperPeaks.bed_pad.bed.tmp" has size 0 issue

Issue - State: open - Opened by shanwai1234 about 4 years ago - 1 comment

#84 - Error determining peaks for anchor inference

Issue - State: open - Opened by AnaAzambuja about 4 years ago - 3 comments

#83 - HiChIP vs HiC input?

Issue - State: open - Opened by Mlad22 over 4 years ago - 2 comments

#82 - IOError: [Errno 2] No such file or directory: .log

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

#81 - .cool format output

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

#80 - --macs2-string parameter: can I use --control?

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

#79 - outputing statistics different with the qcreport

Issue - State: open - Opened by Wenbin-Wang almost 5 years ago - 2 comments

#78 - hichipper in CALL mode

Issue - State: open - Opened by md1587 almost 5 years ago - 1 comment

#77 - outputing statistics about anchor peaks

Issue - State: open - Opened by armenabnousi about 5 years ago - 1 comment

#76 - hichipper into .hic file

Issue - State: open - Opened by AnaAzambuja about 5 years ago - 1 comment

#75 - Issue with MACS Output

Issue - State: open - Opened by jlpulice about 5 years ago - 10 comments

#74 - Testing a version for background sample processing

Pull Request - State: closed - Opened by caleblareau about 5 years ago

#73 - ERROR: Missing hic_results or bowtie_results files for H446-rep

Issue - State: closed - Opened by jlpulice about 5 years ago - 2 comments

#72 - no mango file

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

#71 - Parameters questions

Issue - State: closed - Opened by skytguuu over 5 years ago - 4 comments

#70 - install issue

Issue - State: closed - Opened by skytguuu over 5 years ago

#69 - No qc reports

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

#68 - Double counting validParis

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

#67 - chip-seq input question of Hichipper

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

#66 - Hichipper Inter-chromosomal Loop Statistics

Issue - State: open - Opened by bdecker01 over 5 years ago - 2 comments

#65 - HQ Unique Mapped more than Total PETs???

Issue - State: open - Opened by JungWoongJae almost 6 years ago

#64 - Understanding the output

Issue - State: open - Opened by gouthamatla almost 6 years ago

#63 - Hicpro files

Pull Request - State: closed - Opened by 0xaf1f almost 6 years ago - 6 comments

#62 - Read counts in anchors

Issue - State: open - Opened by gouthamatla almost 6 years ago

#61 - Integration of replicates for HiChIP data

Issue - State: open - Opened by yhx-tj almost 6 years ago

#60 - Error in { : task 1 failed - "need at least four unique 'x' values"

Issue - State: open - Opened by ghost almost 6 years ago

#59 - Error using GRCh38.p12 human genome assembly

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

#58 - Error in hichipper Rscript qc Report

Issue - State: open - Opened by boconnell89 almost 6 years ago - 2 comments

#57 - Hichipper on DNase/Mnase type of data (no Resfrag required)

Issue - State: open - Opened by gundalav almost 6 years ago - 1 comment

#56 - About the pre processing / RM_DUP = 0

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

#55 - .rds not generated

Issue - State: open - Opened by aperreault almost 6 years ago - 2 comments

#54 - Error in { : task 1 failed - "need at least four unique 'x' values" ; Calls: %do% -> <Anonymous>

Issue - State: closed - Opened by vidaletal almost 6 years ago - 2 comments

#53 - the difference between .interaction.txt.gz and .filt.intra.loop_counts.bedpe

Issue - State: open - Opened by WenChangYu about 6 years ago - 1 comment

#52 - could not find function "endsWith"

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

#51 - *_allValidPairs: No such file or directory

Issue - State: closed - Opened by DoaneAS about 6 years ago - 4 comments

#50 - --make-ucsc flag error

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

#49 - Error in { : task 1 failed - "incorrect number of dimensions" Calls: %do% -> <Anonymous> Execution halted

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

#48 - inputting bam file - 'one.filt.intra.loop_counts.bedpe' does not exist in current working directory

Issue - State: open - Opened by armenabnousi about 6 years ago - 1 comment

#47 - ERROR: macs2 peak calling was not successful

Issue - State: open - Opened by aperreault about 6 years ago - 12 comments

#46 - Error message regarding 'x' values

Issue - State: open - Opened by uklejaj over 6 years ago - 3 comments

#45 - question about error message

Issue - State: closed - Opened by jakeukleja over 6 years ago - 2 comments

#44 - Provided hg19 restriction fragment file includes 0bp entry

Issue - State: open - Opened by afrendeiro over 6 years ago - 1 comment

#43 - R dependencies are hard to figure out

Issue - State: open - Opened by mpschr over 6 years ago - 12 comments

#42 - Add option to keep temporary files

Issue - State: closed - Opened by afrendeiro over 6 years ago - 3 comments

#41 - Error in .Call2("NCList_find_overlaps_in_groups", start(q), end(q), q_space

Issue - State: closed - Opened by dongxiaota over 6 years ago - 2 comments

#40 - Error in .Call2("NCList_find_overlaps_in_groups", start(q), end(q)

Issue - State: closed - Opened by dongxiaota over 6 years ago

#39 - Data test exception

Issue - State: open - Opened by tiagochst over 6 years ago - 3 comments

#38 - About html report

Issue - State: open - Opened by werhoog over 6 years ago - 1 comment

#37 - Error in { : task 1 failed - "need at least four unique 'x' values"

Issue - State: closed - Opened by cjt5 over 6 years ago - 6 comments

#36 - About output file of *****.gz.txt

Issue - State: closed - Opened by werhoog over 6 years ago - 2 comments

#35 - About Macs2 parameter

Issue - State: open - Opened by werhoog over 6 years ago - 8 comments

#34 - .yaml round trip

Issue - State: closed - Opened by caleblareau over 6 years ago

#33 - If there any output file about peak calling

Issue - State: closed - Opened by werhoog over 6 years ago - 2 comments

#32 - Rscript requirementsInstall.R fails with error in install.packages

Issue - State: closed - Opened by sowmyaiyer over 6 years ago - 1 comment

#31 - Bedtools does not exist, but we need it

Issue - State: closed - Opened by werhoog over 6 years ago - 2 comments

#30 - Facile integration to WashU genome browser

Issue - State: closed - Opened by caleblareau over 6 years ago - 1 comment

#29 - Hichipper with HiCUP input

Issue - State: open - Opened by rdali over 6 years ago - 3 comments

#28 - Use HiC-Pro allValidPairs as input

Issue - State: open - Opened by martinaryee almost 7 years ago - 7 comments
Labels: enhancement

#27 - ERROR: Missing hic_results or bowtie_results files for sample

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

#26 - Incomplete HTML output in test data and real data.

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

#25 - Warning messages in QC report generation

Issue - State: closed - Opened by 0xaf1f almost 7 years ago - 2 comments
Labels: enhancement

#24 - Rendering HTML reports

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

#23 - empty interaction

Issue - State: closed - Opened by lijiacd985 almost 7 years ago - 7 comments

#22 - About the *.filt.intra.loop_counts.bedpe format

Issue - State: closed - Opened by lijiacd985 about 7 years ago - 4 comments

#21 - Add a Gitter chat badge to README.md

Pull Request - State: closed - Opened by gitter-badger about 7 years ago - 1 comment

#20 - Added regular expression to discard unnecessary input files

Pull Request - State: closed - Opened by caleblareau about 7 years ago

#19 - support absolute file paths

Issue - State: closed - Opened by caleblareau over 7 years ago - 1 comment
Labels: bug

#18 - chipseq input

Issue - State: closed - Opened by sb5169 over 7 years ago - 2 comments

#17 - "Column index must be at most 0 if positive, not 1" error

Issue - State: closed - Opened by stayingsong over 7 years ago - 4 comments

#16 - Can't get right results for simple usage example

Issue - State: closed - Opened by Jiluzhang over 7 years ago - 3 comments

#15 - Inflated alignment stats

Issue - State: open - Opened by caleblareau over 7 years ago - 3 comments

#14 - REpairs file

Issue - State: closed - Opened by caleblareau over 7 years ago - 1 comment

#13 - v0.4.4 < version < v0.5.6 -- duplicates

Issue - State: closed - Opened by caleblareau over 7 years ago - 1 comment
Labels: enhancement

#12 - describe scenarios in the artwork in parameter exp.

Issue - State: closed - Opened by caleblareau over 7 years ago

#11 - bedtools test isn't good

Issue - State: closed - Opened by caleblareau over 7 years ago - 1 comment
Labels: bug

#10 - qc reports update for version 0.5.0

Issue - State: closed - Opened by caleblareau over 7 years ago

#9 - UCSC loop compatibility

Issue - State: closed - Opened by caleblareau over 7 years ago - 2 comments
Labels: enhancement

#8 - memory issues

Issue - State: closed - Opened by caleblareau over 7 years ago

#7 - split files in hicpro

Issue - State: closed - Opened by skyingg over 7 years ago - 10 comments
Labels: enhancement

#6 - keep samples flag

Issue - State: closed - Opened by caleblareau over 7 years ago - 1 comment
Labels: enhancement

#5 - permissions associated with making QC report

Issue - State: closed - Opened by caleblareau over 7 years ago - 1 comment

#4 - Absolute file path

Issue - State: closed - Opened by caleblareau over 7 years ago - 1 comment

#3 - merge attempt2

Pull Request - State: closed - Opened by caleblareau almost 8 years ago

#2 - merge per MJA edits

Pull Request - State: closed - Opened by caleblareau almost 8 years ago - 1 comment

#1 - README suggestion: Add workflow overview figure

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

GitHub / aryeelab/hichipper issues and pull requests