jianhong/ATACseqQC issues and pull requests

#58 - Clear loaded tracks in IGVSnapshot.R

Pull Request - State: closed - Opened by Sfeng666 7 months ago - 1 comment

#57 - Optimizing Time and Memory Usage for Large BAM Files

Issue - State: open - Opened by FarzanehRah 11 months ago - 6 comments

#56 - Error in TSSEscore calculation

Issue - State: closed - Opened by pai-vlc about 1 year ago - 15 comments

#55 - should the original bam be deduped and chrM deleted for the analysis of fragSizeDist()?

Issue - State: closed - Opened by yjiakang over 1 year ago - 2 comments

#54 - Interpreting the outputs of the function TSSEscore() comparing to the reference from ENCODE

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

#53 - merge master to staging

Pull Request - State: closed - Opened by jianhong almost 2 years ago

#52 - Read the shifted bam and continue the QC analysis

Issue - State: open - Opened by XiaoyuZhan520 about 2 years ago - 7 comments

#51 - Output bam files become smaller after shiftGAlignmentsList

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

#50 - different TSS.filter values affect the signals showing on the heatmap

Issue - State: open - Opened by hyjforesight over 2 years ago - 1 comment

#49 - NA values in sigs makes heatmap not completed

Issue - State: closed - Opened by hyjforesight over 2 years ago - 4 comments

#48 - Error: subscript contains invalid names for splitGAlignmentsByCut() function

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

#47 - Strange TSS Enrichment Result

Issue - State: open - Opened by astarr97 over 2 years ago - 1 comment

#46 - What does the x axis mean for Nucleosome Free Regions (NFR) score plot?

Issue - State: closed - Opened by hyjforesight over 2 years ago - 3 comments

#45 - Question about the read filtering by bamQC

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

#44 - Question about bamQC

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

#43 - Processing multiple bam files at once

Issue - State: closed - Opened by etiennedanis over 3 years ago - 2 comments

#42 - splitBam fragment sizes for nucleosome-free DNA

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

#41 - splitGAlignmentsByCut Error in value[[3L]](cond) : 'mergeBam' 'destination' exists, 'overwrite' is FALSE destination: splitBam/NucleosomeFree.bam

Issue - State: open - Opened by rafet2005 over 3 years ago - 8 comments

#40 - Problem with shiftGAlignmentsList()

Issue - State: open - Opened by jingyu0602 almost 4 years ago - 2 comments

#39 - How do I read a BAM file？

Issue - State: open - Opened by BeyondMyPast228 almost 4 years ago - 1 comment

#38 - splitBam return a asBam error

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

#37 - shiftGAlignmentsList() error

Issue - State: open - Opened by hirokomatsui almost 4 years ago - 1 comment

#36 - CIGAR and query sequence are of different length, as.Bam truncated input

Issue - State: closed - Opened by csittz almost 4 years ago

#35 - plot correlation is not symmetric

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

#34 - estimateLibComplexity error

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

#33 - inconsistencies between the package code and user guide

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

#32 - Error on running splitBam

Issue - State: closed - Opened by hchetia about 4 years ago - 13 comments

#31 - Pls help with the error... I am using hg38

Issue - State: open - Opened by hjack123 about 4 years ago - 1 comment

#30 - adjusting readBamFile output for plotCorrelation

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

#29 - factorFootprints error on system.file("extdata", "GL1.bam",package="ATACseqQC")

Issue - State: open - Opened by tinavisnovska about 4 years ago - 2 comments

#28 - phastCons100way.UCSC.hg19 equivalent for mm10 ?

Issue - State: open - Opened by Just08 about 4 years ago - 7 comments

#27 - Remove interactive() in readBamFile.R

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

#26 - Fix wrong index assgined in gal1

Pull Request - State: closed - Opened by ycl6 over 4 years ago - 4 comments

#25 - error in factorFootprints function

Issue - State: closed - Opened by nevelsk90 over 4 years ago - 1 comment

#24 - splitGAlignmentsByCut 'mergeBam' error

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

#23 - A typo at readBamFile.Rd

Pull Request - State: closed - Opened by PollyTikhonova over 4 years ago - 1 comment

#22 - shiftGAlignmentsList after samtools fixmate error

Issue - State: closed - Opened by Hdang1234 over 4 years ago - 14 comments

#21 - Question about readBamFile function

Issue - State: open - Opened by El-Castor over 4 years ago - 20 comments

#20 - How to normalize cut-site probability between samples

Issue - State: open - Opened by kshimizu64928 almost 5 years ago

#19 - error running factorFootprints -- evaluations nested too deeply

Issue - State: open - Opened by magruca almost 5 years ago

#18 - treated as unmapped - splitGAlignmentsByCut

Issue - State: open - Opened by yurasong about 5 years ago - 2 comments

#17 - factorFootprints 'seqnames' issue

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

#16 - TF footprint figure

Issue - State: open - Opened by kshimizu64928 over 5 years ago

#15 - shiftGAlignmentsList Error

Issue - State: open - Opened by samiragarwala over 5 years ago - 3 comments

#14 - How the cut-site probability is calculated?

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

#13 - error when install ATACseqQC

Issue - State: open - Opened by wangjiawen2013 almost 6 years ago - 7 comments

#12 - Adjust the read start sites of mouse data

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

#11 - single reads and distal regions

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

#10 - no "estimateLibComplexity"

Issue - State: open - Opened by marong0511 almost 6 years ago - 3 comments

#9 - Update estimateLibComplexity.R

Pull Request - State: closed - Opened by alexyfyf over 6 years ago - 4 comments

#8 - Update NAMESPACE

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

#7 - replace ds.mincount.bootstrap with ds.rSAC.bootstrap

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

#6 - Error when ATACseqQC load preseqR function ds.mincount.bootstrap

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

#5 - replace any NA with 0 in sel.gr$score

Pull Request - State: closed - Opened by jakevc over 6 years ago - 1 comment

#4 - Error : object 'gscores' is not exported by 'namespace:GenomicScores'

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

#3 - shiftGAlignmentsList time

Issue - State: open - Opened by josruirod over 6 years ago - 4 comments

#2 - Issue: loading bam file using readBamFile uses huge amount of memory causing crashes

Issue - State: open - Opened by zsteve over 6 years ago - 14 comments

#1 - Request: Supporting BamFile and BamFileList as `bamFiles` arg

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

GitHub / jianhong/ATACseqQC issues and pull requests