nanoporetech/remora issues and pull requests

#104 - 80% accuracy threshold intepretation

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

#103 - input data for raw signal analysis

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

#102 - Strand-specific analysis of modified oligos

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

#101 - AttributeError in Read.add_alignment method of remora/io.py

Issue - State: closed - Opened by harikaurel over 1 year ago - 1 comment

#100 - Hardware requirements for `remora analyze plot ref_region`

Issue - State: closed - Opened by replikation over 1 year ago - 1 comment

#99 - Training Dataset

Issue - State: closed - Opened by aCoalBall over 1 year ago - 1 comment

#98 - Removing specific chunks from training by read_id and mod position

Issue - State: closed - Opened by andrewgalbraith21 over 1 year ago - 3 comments

#97 - novel modifications

Issue - State: closed - Opened by Taojianchang over 1 year ago - 5 comments

#96 - model training with one sample

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

#95 - installation issue

Issue - State: closed - Opened by kenneditodd over 1 year ago - 5 comments

#94 - All context mod bases from dorado for duplex reads

Issue - State: closed - Opened by gwl2 over 1 year ago - 3 comments

#93 - Is the MM tag correctly encoded for reverse-strand reads?

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

#92 - remore infer error

Issue - State: closed - Opened by HITzhongyu over 1 year ago - 1 comment

#91 - Sample data to test new models

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

#90 - remora training unstable

Issue - State: closed - Opened by Yijun-Tian over 1 year ago - 8 comments

#89 - m5c interference

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

#88 - Remora mod model for guppy

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

#87 - Remora R9.4.1 5mC+5hmC benchmarks

Issue - State: closed - Opened by billytcl over 1 year ago - 3 comments

#86 - Model not found

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

#85 - remora RNA mod test failed

Issue - State: closed - Opened by vetmohit89 over 1 year ago - 9 comments

#84 - Difference about rescale between tombo and remora

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

#83 - Error when running remora infer duplex_from_pod5_and_bam in GPU

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

#82 - Error while using remora model

Issue - State: closed - Opened by touala over 1 year ago - 5 comments

#81 - questions about annotation

Issue - State: closed - Opened by kewei2019 over 1 year ago - 1 comment

#80 - Mixing data from different runs for training

Issue - State: closed - Opened by drivenbyentropy over 1 year ago - 3 comments

#79 - inference enhancement when using GPU

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

#78 - remora installation error

Issue - State: closed - Opened by vetmohit89 almost 2 years ago - 10 comments

#77 - Questions about 'analyze' and 'rough-rescale' option

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

#76 - Problem of data prepare on version 2.1.1

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

#75 - Support for legacy kmer level tables

Issue - State: closed - Opened by CodingKaiser almost 2 years ago - 3 comments

#74 - assign motif with degenerate code

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

#73 - read length for model training

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

#72 - How to use model "res_dna_r941_min_modbases-all-context_v001.cfg" from rerio

Issue - State: closed - Opened by fsnibs10 almost 2 years ago - 1 comment

#71 - Annotation of data

Issue - State: closed - Opened by kewei2019 almost 2 years ago - 3 comments

#70 - Question: base modification detection for direct RNA sequencing data

Issue - State: closed - Opened by yzhang-github-pub almost 2 years ago - 1 comment

#69 - Move table discordant with basecalls

Issue - State: closed - Opened by Joshmoss11 almost 2 years ago - 2 comments

#68 - pip install ont-remora still at 2.0.0

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

#67 - remora infer doesn't work properly on my computer

Issue - State: closed - Opened by Yijun-Tian almost 2 years ago - 16 comments

#66 - Multiple dataset preparation questions

Issue - State: closed - Opened by jorisbalc almost 2 years ago - 3 comments

#65 - "invalid syntax" when running model train

Issue - State: closed - Opened by kewei2019 almost 2 years ago - 5 comments

#64 - user friendly guide

Issue - State: closed - Opened by Bessem06 almost 2 years ago - 3 comments

#63 - Train on any context for 6mA and 5mC at the same time

Issue - State: closed - Opened by Yijun-Tian almost 2 years ago - 5 comments

#62 - Questions regarding workflow for novel modifications

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

#61 - Long runtime when using remora models

Issue - State: closed - Opened by mvolar almost 2 years ago - 5 comments

#60 - Seperating fast5 format files?

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

#59 - Bonito unable to read modified base remora torch models

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

#58 - Possible bug in code

Issue - State: closed - Opened by tcb72 almost 2 years ago - 1 comment

#57 - Correct workflow for preparing mapped .bam files?

Issue - State: closed - Opened by jorisbalc almost 2 years ago - 9 comments

#56 - Remora dataset prepare memory scaling on clusters

Issue - State: closed - Opened by mvolar almost 2 years ago - 5 comments

#55 - --focus-reference-positions flag

Issue - State: closed - Opened by Joshmoss11 almost 2 years ago - 1 comment

#54 - DNA m6A calling support?

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

#53 - Found no BAM records in dataset preparation

Issue - State: closed - Opened by xph9876 about 2 years ago - 5 comments

#52 - Suggested coverage for model training

Issue - State: closed - Opened by mvolar about 2 years ago - 3 comments

#51 - Remora modified base pre-trained model won't download

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

#50 - questions: remora models for R9.4 in guppy, bonito, and dorado

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

#49 - Any support for 5hmC on the newest Remora models for r9.4.1?

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

#48 - RNA Support

Issue - State: closed - Opened by marcus1487 about 2 years ago - 1 comment

#47 - direct download links ?

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

#46 - How do I use Remora v2 with Guppy?

Issue - State: closed - Opened by billytcl about 2 years ago - 3 comments

#45 - How to label positive site when I wanna train my own model

Issue - State: closed - Opened by JeremyQuo about 2 years ago - 3 comments

#44 - Install ont-remora==2.0.0 failed, due to pod5 install failed

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

#43 - remora model calls different from cell samples and blood samples

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

#42 - How to draw histogram plots of modified base probabilities using Ml probability tag in modified BAM file?

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

#41 - Is remora 5hmC/5mC ready for "prime time"?

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

#40 - How megalodon get the threshold when load remora model

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

#39 - How to interpret 'remora model list_pretrained'/model selection?

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

#38 - Data preparation scripts for Remora models with random bases

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

#37 - Question about data preparation for training model

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

#36 - Remora model train error

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

#35 - Error when running with remora with megalodon

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

#34 - Model improvement questions

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

#33 - question about 'remora infer' command

Issue - State: closed - Opened by Flower9618 over 2 years ago - 1 comment

#32 - About the pre-trained models

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

#31 - Running Megalodon for Remora 5mC_all_context_sup_r1041_e82 model

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

#30 - about balanced_batch

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

#29 - Insect 5hmC values anomalous

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

#28 - some basic question about using remora

Issue - State: closed - Opened by charliechen912ilovbash over 2 years ago - 5 comments

#27 - How to use megalodon with ONNX model?

Issue - State: closed - Opened by cvermeulen88 over 2 years ago - 1 comment

#26 - R10.4 250bps signal to base mapping

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

#25 - Correct model to use for 5hmC calling

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

#24 - 'Remora model list_pretrained'

Issue - State: closed - Opened by Flower9618 over 2 years ago - 5 comments

#23 - what kind of modification sites can be detected?

Issue - State: closed - Opened by defendant602 over 2 years ago - 1 comment

#22 - Error while installing remora

Issue - State: closed - Opened by AzlanNI over 2 years ago - 16 comments

#21 - how to interpret the results from "remora infer from_taiyaki_mapped_signal"

Issue - State: closed - Opened by jon-xu almost 3 years ago - 10 comments

#20 - typo in the README

Issue - State: closed - Opened by jon-xu almost 3 years ago - 1 comment

#19 - Regarding "--motif N 0"

Issue - State: closed - Opened by hukai916 almost 3 years ago - 2 comments

#18 - Multiple GPU device

Issue - State: open - Opened by vahidAK almost 3 years ago - 2 comments

#17 - Accuracy about Remora

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

#16 - quick question

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

#15 - Various questions about Remora

Issue - State: closed - Opened by tcb72 almost 3 years ago - 9 comments

#14 - R10.4 settings recommendations

Issue - State: closed - Opened by pwh124 almost 3 years ago - 2 comments

#13 - remora model with multiple modifications

Issue - State: closed - Opened by hd2326 almost 3 years ago - 4 comments

#12 - Installation of taiyaki

Issue - State: closed - Opened by pwh124 almost 3 years ago - 7 comments

#11 - Training remora for use with bonito

Issue - State: closed - Opened by snajder-r almost 3 years ago - 1 comment
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GitHub / nanoporetech/remora issues and pull requests