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GitHub / rrazaghi/modbamtools issues and pull requests

#40 - Only plot command working

Issue - State: open - Opened by skranz0 about 1 year ago

#39 - Installation issue /modbamtools

Issue - State: open - Opened by Jordi0102 over 1 year ago - 1 comment

#38 - KeyError: 'gene_id'

Issue - State: open - Opened by partha434 over 1 year ago - 1 comment

#37 - modbamtools plot command will append on more output if the same prefix is used

Issue - State: open - Opened by pwh124 almost 2 years ago

#36 - PDF output no longer works

Issue - State: open - Opened by pwh124 almost 2 years ago

#35 - Heterogeneity calculation does not work without a GTF file

Issue - State: open - Opened by pwh124 almost 2 years ago - 5 comments

#34 - No clustering if a GTF isn't also used as an input

Issue - State: open - Opened by pwh124 almost 2 years ago

#33 - Add unphased BAM to example files for testing purposes

Issue - State: open - Opened by pwh124 almost 2 years ago

#32 - BAM haplotyping requirement

Issue - State: open - Opened by pwh124 almost 2 years ago

#31 - Installation issues

Issue - State: open - Opened by pwh124 almost 2 years ago

#30 - How to color samples of the same group with the same color?

Issue - State: open - Opened by kaanokay almost 2 years ago

#29 - Issues with using the modbamtools plot

Issue - State: open - Opened by olaraym almost 2 years ago

#28 - ValueError: If mode is 'interp', window_length must be less than or equal to the size of x.

Issue - State: open - Opened by rl4940 almost 2 years ago - 2 comments

#27 - Clustering failure produces error message

Issue - State: open - Opened by rowanhowellGE almost 2 years ago

#26 - ValueError: If mode is 'interp', window_length must be less than or equal to the size of x.

Issue - State: closed - Opened by rainwala almost 2 years ago - 1 comment

#25 - mod bam with both 5mC and 5hmC?

Issue - State: open - Opened by gwonshin almost 2 years ago

#24 - Plotting a BED file - parse_bed_rectangle_gl function

Issue - State: open - Opened by steven-solar about 2 years ago - 2 comments

#23 - IndexError: list index out of range

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

#22 - How to use modbamtools cluster for multiple modbams?

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

#21 - calcmeth sample size concern

Issue - State: open - Opened by Yijun-Tian about 2 years ago

#20 - parse_bed_rectangle_gl function is missing

Issue - State: open - Opened by Priyesh000 about 2 years ago - 1 comment

#19 - How to sort Grch37 gtf file ?

Issue - State: closed - Opened by xiucz about 2 years ago - 1 comment

#18 - Correct format for plotting multiple bams

Issue - State: closed - Opened by 690645258 over 2 years ago - 3 comments

#17 - Installing modbamtools/0.4.8 on python/3.10 lacking package of libmodbampy

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

#16 - automatically adjust spacing and marker size in single reads

Issue - State: open - Opened by rrazaghi over 2 years ago
Labels: enhancement

#15 - expand methylation smoothing methods

Issue - State: open - Opened by rrazaghi over 2 years ago
Labels: enhancement

#14 - ValueError: If mode is 'interp', window_length must be less than or equal to the size of x.

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

#13 - add cluster assignment as a bam tag to output

Issue - State: open - Opened by rrazaghi over 2 years ago
Labels: enhancement

#12 - Installation on ubuntu 20.04

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

#11 - 3+ haplotypes?

Issue - State: closed - Opened by colindaven over 2 years ago - 4 comments
Labels: enhancement

#10 - error loading taidx file

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

#9 - error running modbamtools

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

#8 - add WebGL support for html outputs

Issue - State: closed - Opened by rrazaghi over 2 years ago - 1 comment
Labels: enhancement

#7 - add min sample size option to clustering command

Issue - State: open - Opened by rrazaghi over 2 years ago
Labels: enhancement

#6 - add --color to plot

Issue - State: open - Opened by rrazaghi over 2 years ago
Labels: enhancement

#5 - update pytest

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

#4 - add documentation for heterogeneity module

Issue - State: open - Opened by rrazaghi over 2 years ago
Labels: documentation

#3 - Python 3.9 3.10 support

Issue - State: closed - Opened by rrazaghi over 2 years ago - 1 comment
Labels: enhancement

#2 - Add font scale

Issue - State: closed - Opened by rrazaghi over 2 years ago - 1 comment
Labels: enhancement

#1 - legend missing in graph

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