PengNi/ccsmeth issues and pull requests

#50 - call_mod error in vision 0.5.0

Issue - State: open - Opened by Songmg-Nwafu 6 months ago - 1 comment

#49 - Results based on count and model at the genome level is different

Issue - State: open - Opened by HITzhongyu 10 months ago

#48 - IndexError while running ccsmeth call_mods

Issue - State: open - Opened by suvi93 11 months ago - 10 comments

#47 - Extract features file

Issue - State: open - Opened by yycunc 11 months ago - 2 comments

#46 - Index error during align_reads in denovo mode

Issue - State: open - Opened by Surbhigrewal 12 months ago - 2 comments

#45 - How to train a model to infer the site-level methylation frequency

Issue - State: closed - Opened by Songmg-Nwafu about 1 year ago - 2 comments

#44 - A question about the frequency threshold determination

Issue - State: closed - Opened by Wyinghao about 1 year ago - 3 comments

#43 - Methylation Data Labels Problems

Issue - State: closed - Opened by XiYee23 about 1 year ago

#42 - calling modifications on Pacbio Revio platform

Issue - State: open - Opened by eric-hy about 1 year ago - 1 comment

#41 - Training error

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

#40 - ccsmeth call_mods: indexError and TypeError

Issue - State: closed - Opened by dnalinkbi over 1 year ago - 9 comments

#39 - Normalization

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

#38 - All reads are skipped/failed

Issue - State: open - Opened by dnalinkbi over 1 year ago - 4 comments

#37 - Process stuck when split the data.

Issue - State: closed - Opened by cosineDaDa0623 over 1 year ago - 4 comments

#36 - Modify the number of the layers

Issue - State: open - Opened by RahelehSalehi over 1 year ago - 2 comments

#35 - RuntimeError: cuDNN error: CUDNN_STATUS_EXECUTION_FAILED

Issue - State: open - Opened by rl4940 over 1 year ago - 2 comments

#34 - 卡在11%不动了

Issue - State: closed - Opened by rl4940 over 1 year ago - 2 comments

#33 - CCSMETH TRAIN

Issue - State: open - Opened by olaraym over 1 year ago - 3 comments

#32 - call strand-specific methylation

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

#31 - Call modification

Issue - State: open - Opened by RahelehSalehi over 1 year ago - 24 comments

#30 - Extract features file structure

Issue - State: open - Opened by RahelehSalehi over 1 year ago - 15 comments

#29 - confusion about the traditional ccsmeth procedure

Issue - State: closed - Opened by wzhang42 almost 2 years ago - 2 comments

#28 - setting temp folder for samtools

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

#27 - never ending run

Issue - State: open - Opened by romaingroux about 2 years ago - 2 comments
Labels: bug

#26 - stderr/log optimization

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

#25 - How to avoid call_freqb aggregate-mode using all cores automatically

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

#24 - model for CHG or CHH with HiFi reads

Issue - State: closed - Opened by baozg about 2 years ago - 13 comments
Labels: enhancement

#23 - A question about the output file

Issue - State: closed - Opened by hunkui1 about 2 years ago - 2 comments

#22 - A question about BedTools

Issue - State: closed - Opened by hunkui1 about 2 years ago - 12 comments

#21 - add submodule for model_ckpt downloading

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

#20 - optimize ccsmeth call_mods procedure

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

#19 - No local packages or working download links found for ('torch<=1.7.0,>=1.2.0')

Issue - State: closed - Opened by mikeds211 over 2 years ago - 1 comment

#18 - how about cpg_tools of Pacbio

Issue - State: closed - Opened by hmyh1202 over 2 years ago - 6 comments

#17 - Import error

Issue - State: closed - Opened by priyambial123 over 2 years ago - 2 comments

#16 - Where is the master - models

Issue - State: closed - Opened by hunkui1 over 2 years ago - 6 comments

#15 - allele-specific methylation

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

#14 - Installing ccsmeth

Issue - State: closed - Opened by priyambial123 over 2 years ago - 1 comment

#13 - Question:types of input, old data or just HiFi?

Issue - State: closed - Opened by mikeds211 over 2 years ago - 9 comments

#12 - about vocub_size

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

#11 - How to write a Dataset that reduces memory usage and fits in DistributedSampler?

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

#10 - multi GPU training and testing

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

#9 - Output reference CGs or not when there are SNVs at corresponding sites of reads

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

#8 - empty output of ccsmeth extract command

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

#7 - Call plant methylation using hg002 trained model？

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

#6 - ccsmeth train

Issue - State: closed - Opened by SarahChen0401 over 2 years ago - 1 comment

#5 - add pbmm2 as subreads aligner

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

#4 - ccsmeth call_mods

Issue - State: closed - Opened by SarahChen0401 over 2 years ago - 4 comments

#3 - interpret features.zscore.fb.depth1.call_mods.tsv

Issue - State: closed - Opened by SarahChen0401 over 2 years ago - 2 comments

#2 - TypeError: 'tuple' object does not support item assignment

Issue - State: closed - Opened by SarahChen0401 over 2 years ago - 2 comments

#1 - install error

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

GitHub / PengNi/ccsmeth issues and pull requests