bioinfomaticsCSU/deepsignal issues and pull requests

#86 - Need for 6mA detection package

Issue - State: open - Opened by Bin-Ma 10 months ago

#85 - No output with DeepSignal Extract Command

Issue - State: open - Opened by kewei2019 over 1 year ago - 2 comments

#84 - What is this file: bn_17.sn_360.epoch_9.ckpt.data-00000-of-00001

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

#83 - Added sequences to a total of 0 reads.

Issue - State: open - Opened by Arkadiy-Garber almost 2 years ago - 1 comment

#82 - Problem about Deepsignal in 6mA detection.

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

#81 - Do I need Whole Genome Amplified dataset?

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

#80 - Issue with downloading E.coli Nanopore data

Issue - State: open - Opened by Bessyyi almost 3 years ago

#79 - Training of a custom model

Issue - State: closed - Opened by hukai916 almost 3 years ago - 4 comments

#78 - visualization the data

Issue - State: open - Opened by Fatihlrcfs almost 3 years ago - 5 comments

#77 - Questions about sequence module

Issue - State: closed - Opened by Flower9618 about 3 years ago - 1 comment

#76 - extract_features fails on all files

Issue - State: closed - Opened by jamesabbott about 3 years ago - 4 comments

#75 - data problem

Issue - State: closed - Opened by Xiaoliugogogo about 3 years ago - 7 comments

#74 - Questions on training function of DeepSignal

Issue - State: closed - Opened by PanZiwei about 3 years ago - 5 comments

#73 - unsuccessfully processed reads

Issue - State: closed - Opened by xj-Liang-Olga over 3 years ago - 1 comment

#72 - Trained Models and Yeast?

Issue - State: closed - Opened by JayVaz18 almost 4 years ago - 4 comments

#71 - Where does deepsignal save the temporary files?

Issue - State: closed - Opened by ViHammer almost 4 years ago - 2 comments

#70 - [Bug] DataLoss error while performing methylation calling using GATC model

Issue - State: closed - Opened by atger almost 4 years ago - 11 comments

#69 - What's the difference between the CpG model and the GATC model?

Issue - State: closed - Opened by 123chenshixin almost 4 years ago - 1 comment

#68 - Updating DeepSignal? [question]

Issue - State: closed - Opened by davidebolo1993 almost 4 years ago - 7 comments

#67 - RNA methylation calling

Issue - State: open - Opened by SilvanHaelg almost 4 years ago - 8 comments

#66 - Using multiple fast5 dirs

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

#65 - guppy_basecaller in README.md instructions

Issue - State: closed - Opened by kxk302 about 4 years ago - 2 comments

#64 - Training model with more than 2 classes

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

#63 - Available trained model on E.coli data?

Issue - State: closed - Opened by mandichen about 4 years ago - 2 comments

#62 - ModuleNotFoundError: No module named 'txt_formater'

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

#61 - Training or calling with multiple GPU

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

#60 - Error while running call mods using GATC model

Issue - State: closed - Opened by onkar2470 over 4 years ago - 2 comments

#59 - defining methyl_label

Issue - State: closed - Opened by akk01 over 4 years ago - 1 comment

#58 - The feature extraction output 'signal_means' are different from the value in fast5 files.

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

#57 - Problems with call_mods

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

#56 - Information about deepsignal

Issue - State: closed - Opened by cyber-ux over 4 years ago - 16 comments

#55 - The original FAST5 file looked for 6mA loci

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

#54 - Albacore paramter used for basecalling

Issue - State: closed - Opened by akk01 over 4 years ago - 2 comments

#53 - Example training and validation data

Issue - State: closed - Opened by akk01 over 4 years ago - 6 comments

#52 - Genome sequence in feature extraction

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

#51 - wget link for data

Issue - State: closed - Opened by akk01 over 4 years ago - 2 comments

#50 - Question about train dataset

Issue - State: closed - Opened by Jerry-0591 over 4 years ago - 6 comments

#49 - Results of extract features step

Issue - State: closed - Opened by Jerry-0591 over 4 years ago - 5 comments

#48 - Output BED format of call_mods_freq results

Issue - State: closed - Opened by PengNi over 4 years ago - 1 comment
Labels: enhancement

#47 - Error when using newly trained model

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

#46 - How to calculate methylation frequencies from predict probability

Issue - State: closed - Opened by PanZiwei over 4 years ago - 3 comments

#45 - Clarification about filter_samples_by_positions.py

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

#44 - Nanopore data for NA12878

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

#43 - process interrupt

Issue - State: closed - Opened by PengNi over 4 years ago - 2 comments
Labels: bug

#42 - HX1 Data availability

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

#41 - Warning and missing checkpoint with model training on gpu

Issue - State: closed - Opened by pterzian almost 5 years ago - 12 comments

#40 - Deepsingal not running on gpu

Issue - State: closed - Opened by avitalsteiman almost 5 years ago - 4 comments

#39 - insertion methylation level

Issue - State: closed - Opened by Yeeok almost 5 years ago - 1 comment

#38 - Problem while running deepsignal on GPU

Issue - State: closed - Opened by stefanucci-luca almost 5 years ago - 1 comment

#37 - Questions about plant DNA methylation

Issue - State: closed - Opened by LongZhao1992 about 5 years ago - 4 comments

#36 - download problems

Issue - State: closed - Opened by lqsae about 5 years ago - 4 comments

#35 - Feature extraction

Issue - State: closed - Opened by vahidAK about 5 years ago - 1 comment

#34 - Model training outputs many files and still runing

Issue - State: closed - Opened by vahidAK about 5 years ago - 3 comments

#33 - Installation Issue

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

#32 - Model training, feature extraction error.

Issue - State: closed - Opened by vahidAK about 5 years ago - 1 comment

#31 - Result verification

Issue - State: closed - Opened by ritma001 about 5 years ago - 4 comments

#30 - How long does it take to finish 30X human data?

Issue - State: closed - Opened by hd00ljy over 5 years ago - 6 comments

#29 - Don't import tensorflow when extracting features

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

#28 - Bump tensorflow from 1.8.0 to 1.12.2

Pull Request - State: closed - Opened by dependabot[bot] over 5 years ago - 1 comment
Labels: dependencies

#27 - Non-CpG methylation calling

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

#26 - Your paper circle plot

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

#25 - deepsignal extract position file

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

#24 - It would be very nice if you could add cuda option to DeepSignal

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

#23 - How to calculate accuracy and other metrics by evaluate_mods_call.py?

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

#22 - Error while calling mod and assigning threads

Issue - State: closed - Opened by vahidAK over 5 years ago - 10 comments
Labels: bug

#21 - self._sem._semlock._get_value() not implemented error

Issue - State: closed - Opened by ardakdemir over 5 years ago - 5 comments
Labels: bug

#20 - Split extracted_features file and run methylation calling

Issue - State: closed - Opened by vahidAK over 5 years ago - 5 comments
Labels: enhancement

#19 - Multi_read Fast5s

Issue - State: open - Opened by vahidAK over 5 years ago - 2 comments
Labels: enhancement

#18 - use newer tensorflow

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

#17 - Get position of targeted base in reads event table

Issue - State: closed - Opened by pterzian over 5 years ago - 3 comments

#16 - Meaning of cent_signals

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

#15 - Extracting methy_label from fast5 files

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

#14 - Add warning or more test when deleting content of model directory

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

#13 - Training motif specific models

Issue - State: closed - Opened by pterzian over 5 years ago - 10 comments

#12 - How to get my files to basecall

Issue - State: closed - Opened by Hannah1746 over 5 years ago - 5 comments

#11 - model_path

Issue - State: closed - Opened by Hannah1746 over 5 years ago - 4 comments

#10 - Training a new model

Issue - State: closed - Opened by forrest1988 over 5 years ago - 2 comments

#9 - running "deepsignal extract" without tombo.index

Issue - State: closed - Opened by Puputnik almost 6 years ago - 1 comment

#8 - How to detect 6mA methylation using deepsignal?

Issue - State: closed - Opened by tianrenmao almost 6 years ago - 5 comments

#7 - how to train a model

Issue - State: closed - Opened by ShangjinTan almost 6 years ago - 13 comments

#6 - normalize prob0 and prob1 before output

Issue - State: closed - Opened by PengNi almost 6 years ago - 1 comment

#5 - Expected results for example data set?

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

#4 - subprocess won't stop

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

#3 - multiprocessing

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

#2 - add options for RNA

Issue - State: open - Opened by PengNi about 6 years ago

#1 - add a "region" option

Issue - State: open - Opened by PengNi about 6 years ago

GitHub / bioinfomaticsCSU/deepsignal issues and pull requests