Ecosyste.ms: Issues

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GitHub / MiraldiLab/maxATAC issues and pull requests

#142 - Update parser.py

Pull Request - State: open - Opened by ANRudrapatna about 1 month ago

#141 - Update benchmark.py

Pull Request - State: open - Opened by ANRudrapatna about 1 month ago

#140 - Update plot.py

Pull Request - State: open - Opened by ANRudrapatna about 2 months ago

#139 - Update parser.py

Pull Request - State: open - Opened by ANRudrapatna about 2 months ago

#138 - Update benchmark.md

Pull Request - State: open - Opened by ANRudrapatna about 2 months ago

#137 - Update train.md

Pull Request - State: closed - Opened by ANRudrapatna about 2 months ago

#136 - Update predict.md

Pull Request - State: closed - Opened by ANRudrapatna about 2 months ago

#135 - Update train.md

Pull Request - State: closed - Opened by ANRudrapatna about 2 months ago

#134 - Update predict.md

Pull Request - State: closed - Opened by ANRudrapatna about 2 months ago

#133 - Update train.md

Pull Request - State: closed - Opened by ANRudrapatna about 2 months ago

#132 - clarification on the ChIP-seq bigwig needed for training

Issue - State: closed - Opened by plger 3 months ago - 2 comments

#131 - add thread option to prediction

Pull Request - State: open - Opened by XiaotingChen 6 months ago - 2 comments

#130 - Change Path for

Issue - State: closed - Opened by Elfaba 7 months ago - 1 comment

#129 - import error _OrderedEnqueuer_ tensorflow.keras.utils

Issue - State: closed - Opened by martinezvbs 7 months ago - 6 comments

#128 - Error on running prepare: subprocess.CalledProcessError

Issue - State: closed - Opened by Lozzard 10 months ago - 1 comment

#127 - Update prediction_tools.py

Pull Request - State: closed - Opened by ANRudrapatna 10 months ago

#126 - pseudo-bulk

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

#125 - Fixing ModuleNotFoundError: No module named 'keras.utils.data_utils'

Pull Request - State: closed - Opened by XiaotingChen about 1 year ago
Labels: bug

#124 - Update predict.md

Pull Request - State: closed - Opened by ANRudrapatna about 1 year ago - 2 comments

#123 - Update train.md

Pull Request - State: closed - Opened by ANRudrapatna about 1 year ago

#122 - keras error after installation

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

#121 - Update normalize.md

Pull Request - State: closed - Opened by ANRudrapatna over 1 year ago - 2 comments

#120 - Update predict.md

Pull Request - State: closed - Opened by ANRudrapatna over 1 year ago - 1 comment

#119 - `maxATAC` prepare with sc 10X ATAC

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

#118 - Update DEFAULT_BENCHMARKING_BIN_SIZE to align with publication

Pull Request - State: closed - Opened by XiaotingChen over 1 year ago

#117 - pyBigWig values method does not take argument numpy=True

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

#116 - Question about training/testing celltypes

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

#115 - Error on running predict: could not load dynamic library for tensorflow

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

#113 - Publication updates

Pull Request - State: closed - Opened by tacazares about 2 years ago

#112 - Remove hardcoded paths in `maxatac prepare` and in maxatac_data so users can provide custom chromosome sets

Issue - State: closed - Opened by tacazares about 2 years ago - 6 comments
Labels: enhancement

#111 - What is the fourth column in the bed file the variants function produce?

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

#110 - Mm

Pull Request - State: closed - Opened by FaizRizvi over 2 years ago - 1 comment

#109 - Fix flags across functions for consistency

Issue - State: closed - Opened by tacazares over 2 years ago
Labels: bug, enhancement

#107 - Improve `maxatac prepare`

Issue - State: closed - Opened by tacazares over 2 years ago - 1 comment
Labels: bug, enhancement

#106 - Multiprocessing with Ordered Enquerer

Pull Request - State: closed - Opened by FaizRizvi over 2 years ago - 1 comment

#105 - 101 roi generator, documentation, and get_target_matrix function added

Pull Request - State: closed - Opened by tacazares over 2 years ago

#104 - Add tests and set up some Continuous Integration (CI)

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

#103 - Documentation Updates

Pull Request - State: closed - Opened by tacazares over 2 years ago

#101 - Update `maxatac train` and optimize

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

#100 - Graphviz error with `maxatac train`

Issue - State: closed - Opened by tacazares over 2 years ago
Labels: bug

#99 - #97 Update prepare function for scATAC-seq

Pull Request - State: closed - Opened by tacazares over 2 years ago
Labels: bug

#98 - 93 variants parser

Pull Request - State: closed - Opened by tacazares over 2 years ago
Labels: bug, documentation

#97 - `maxatac prepare` issue processing scATAC-seq fragment files

Issue - State: closed - Opened by tacazares over 2 years ago

#96 - `maxatac prepare` erroring out at normalization

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

#95 - #93 fix missing chrom_sizes for ROI based variant predictions

Pull Request - State: closed - Opened by FaizRizvi over 2 years ago

#94 - #93 fix variants.py and associated parser in parser.py

Pull Request - State: closed - Opened by tacazares over 2 years ago
Labels: bug

#93 - variants_bed invalid int value

Issue - State: closed - Opened by hrayjones over 2 years ago - 13 comments
Labels: bug

#91 - Best value to use for thresholds

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

#90 - Interesting observation with predictions: Blacklist update

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

#89 - train.md clarifications

Issue - State: closed - Opened by emiraldi almost 3 years ago
Labels: documentation

#88 - docs/readme/peaks.md disconnect example / arguments

Issue - State: closed - Opened by emiraldi almost 3 years ago - 1 comment
Labels: documentation

#87 - Installation issues with pyBigWig not finding numpy

Issue - State: closed - Opened by tacazares almost 3 years ago

#86 - --agg options for benchmark.md

Issue - State: closed - Opened by emiraldi almost 3 years ago - 2 comments
Labels: documentation

#85 - default for noramlize.md

Issue - State: closed - Opened by emiraldi almost 3 years ago
Labels: documentation

#84 - Benchmarking: separate quantitative and binary evaluation

Issue - State: closed - Opened by emiraldi almost 3 years ago
Labels: documentation, enhancement

#83 - Enhancements: sex chromosome predictions

Issue - State: closed - Opened by emiraldi almost 3 years ago - 2 comments
Labels: enhancement, analysis

#82 - Build AppImage for Linux

Pull Request - State: closed - Opened by michael-kotliar almost 3 years ago - 3 comments

#81 - Final modifications pre-publication submission

Pull Request - State: closed - Opened by tacazares almost 3 years ago - 1 comment

#80 - Finalize Code Base

Issue - State: closed - Opened by FaizRizvi almost 3 years ago - 14 comments

#79 - Refactor

Pull Request - State: closed - Opened by FaizRizvi almost 3 years ago

#78 - Refactor threshold

Pull Request - State: closed - Opened by FaizRizvi almost 3 years ago

#77 - Update peak centric prediction

Issue - State: closed - Opened by tacazares almost 3 years ago

#76 - Refactor par pred

Pull Request - State: closed - Opened by FaizRizvi almost 3 years ago - 1 comment

#75 - Refactor prepare

Pull Request - State: closed - Opened by tacazares almost 3 years ago

#74 - Refactor variant predict

Pull Request - State: closed - Opened by tacazares almost 3 years ago

#73 - Refactor peaks

Pull Request - State: closed - Opened by FaizRizvi almost 3 years ago

#72 - Refactor peaks

Pull Request - State: closed - Opened by tacazares almost 3 years ago

#71 - Write a detailed prediction walkthrough

Issue - State: closed - Opened by tacazares about 3 years ago - 2 comments
Labels: documentation

#70 - Integrate peak calling into prediction code

Issue - State: closed - Opened by tacazares about 3 years ago
Labels: enhancement

#69 - Optimize whole-genome prediction time

Issue - State: closed - Opened by tacazares about 3 years ago - 1 comment
Labels: enhancement

#68 - Optimize min-max normalization memory usage and time

Issue - State: closed - Opened by tacazares about 3 years ago - 1 comment
Labels: enhancement

#67 - Write a maxATAC function to prepare ATAC-seq data from a BAM file and review main pipelines

Issue - State: closed - Opened by tacazares about 3 years ago - 4 comments
Labels: documentation, enhancement

#66 - Implement and document a way to retrieve the required reference data

Issue - State: closed - Opened by tacazares about 3 years ago - 3 comments
Labels: documentation, enhancement

#65 - Docker and install

Issue - State: closed - Opened by FaizRizvi about 3 years ago - 16 comments

#63 - Make sure the maxATAC python package can be installed on python 3.7/3.8/3.9 on both Ubuntu and macOS

Issue - State: closed - Opened by michael-kotliar about 3 years ago - 5 comments
Labels: wontfix

#62 - Refactor. Work in progress

Pull Request - State: closed - Opened by michael-kotliar about 3 years ago - 9 comments

#61 - Preparing for the paper

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

#60 - Develop is59

Pull Request - State: closed - Opened by tacazares about 3 years ago
Labels: bug, test feature

#59 - Remove maxATAC interpretation for independent development

Issue - State: closed - Opened by tacazares about 3 years ago - 2 comments
Labels: bug

#58 - Numpy compatibility for Tensorflow 2.5 and SHAP in interpreting analysis jobs

Issue - State: open - Opened by XiaotingChen about 3 years ago - 2 comments
Labels: bug

#57 - Develop is54

Pull Request - State: closed - Opened by tacazares about 3 years ago

#56 - OSC Node Crash invoked by Kernel Bug

Issue - State: closed - Opened by FaizRizvi over 3 years ago - 1 comment
Labels: bug

#55 - Develop

Pull Request - State: closed - Opened by FaizRizvi over 3 years ago

#54 - Error in how area under the precision recall curve is calculated

Issue - State: closed - Opened by tacazares over 3 years ago
Labels: bug, analysis

#53 - Generate Data for Publication Figures

Issue - State: closed - Opened by tacazares over 3 years ago
Labels: documentation, analysis, data

#52 - Develop cheers

Pull Request - State: closed - Opened by FaizRizvi over 3 years ago

#51 - Develop cheers

Pull Request - State: closed - Opened by FaizRizvi over 3 years ago

#50 - Develop

Pull Request - State: closed - Opened by tacazares over 3 years ago

#49 - Random Precision Benchmarking

Issue - State: closed - Opened by FaizRizvi over 3 years ago - 1 comment

#48 - Develop is46

Pull Request - State: closed - Opened by tacazares over 3 years ago

#47 - Installation errors when using Anaconda and maxATAC TensorFlow2.5

Issue - State: closed - Opened by tacazares over 3 years ago - 1 comment
Labels: bug

#46 - Invalid Interval Bounds Error When Training

Issue - State: closed - Opened by tacazares over 3 years ago
Labels: bug

#45 - Reverse_complement training flag

Issue - State: closed - Opened by FaizRizvi over 3 years ago - 2 comments
Labels: enhancement

#44 - Develop normalize

Pull Request - State: closed - Opened by tacazares over 3 years ago

#43 - Update average documentation + default chroms are autosomal

Pull Request - State: closed - Opened by tacazares over 3 years ago

#42 - Finalize maxATAC v1 ATAC-seq data

Issue - State: closed - Opened by tacazares over 3 years ago - 2 comments
Labels: analysis, data