Ecosyste.ms: Issues

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GitHub / singjc/metagenpipe issues and pull requests

#86 - cluster workfows

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

#85 - Memory Usage for Humann3 genefamilies file

Issue - State: open - Opened by whitleyo about 3 years ago

#84 - Dev owen

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

#83 - Dev owen

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

#82 - Dev owen

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

#81 - [MODIFY] bugfix to snakemake for papermill compile

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

#80 - Dev owen

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

#79 - Dev owen

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

#78 - Dev owen

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

#77 - Dev owen

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

#76 - Dev owen

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

#75 - Dev owen

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

#74 - Dev owen

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

#73 - Dev owen. Humann3 pipeline, with apparent databse version issues

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

#72 - fix SRADownLoad.py for efetch API

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

#71 - add lipid data setup

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

#70 - PE Sampling Full Dataset Update and Publication Figures

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

#69 - [ADD] LR_Classifier_clinical_only_generic.ipynb

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

#68 - merge whitleyo with florabioworks

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

#67 - Dev owen

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

#66 - Dev owen

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

#65 - [MODIFY] Replaced conda installs with mamba

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

#64 - Added WF for running on an HPC cluster

Pull Request - State: closed - Opened by singjc over 3 years ago
Labels: enhancement

#63 - Dev owen

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

#62 - Dev owen

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

#61 - Dev owen

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

#60 - Dev owen

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

#59 - Dev owen

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

#58 - [ADD] LR_Classifier_DE_generic

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

#57 - Dev owen

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

#56 - [ADD] Clinical_correlates_generic.ipynb. added more statistics functi…

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

#55 - Dev owen

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

#54 - Dev owen

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

#53 - Dev owen

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

#52 - Dev owen

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

#51 - Dev owen

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

#50 - Dev owen

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

#48 - Dev owen

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

#47 - Dev owen

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

#46 - Dev owen

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

#45 - Dev owen

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

#44 - Dev owen

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

#43 - Dev owen

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

#42 - [ADD] Add a check in seqtk call for presence of subsampled file, if p…

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

#41 - Dev owen

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

#40 - Dev owen

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

#39 - Dev owen

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

#38 - Dev owen

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

#37 - Dev owen

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

#36 - [ADD] add comparison of subsampling results at various depths for Jie…

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

#35 - Dev owen

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

#34 - Dev owen

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

#33 - Dev owen

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

#32 - Dev owen

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

#31 - Resolve Merge Conflicts and fix bug in run-kneaddata

Pull Request - State: closed - Opened by singjc over 3 years ago
Labels: enhancement

#30 - merge master to dev_owen

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

#29 - Dev owen

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

#28 - Dev owen

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

#27 - Dev owen

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

#26 - Dev owen

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

#25 - Added Paired end mode to kneaddata call

Pull Request - State: closed - Opened by singjc over 3 years ago
Labels: enhancement

#24 - [ADD] Added SRADownLoader to metagenpipe command, and added extra arg…

Pull Request - State: closed - Opened by singjc over 3 years ago
Labels: enhancement

#23 - [ADD] Added option to pass extra args to kneaddata.

Pull Request - State: closed - Opened by singjc over 3 years ago
Labels: enhancement

#22 - Clean Dockerfile, add Kraken2, separate out database download

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

#21 - Sanity Check Experiments

Pull Request - State: closed - Opened by singjc over 3 years ago
Labels: enhancement

#19 - [ADD] add analysis of feature counts in Gupta precompiled data

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

#18 - [ADD] Added unpacking of tar.gz archives.

Pull Request - State: closed - Opened by singjc over 3 years ago
Labels: enhancement

#17 - Repo Cleaning and Added 500k Subsampling Experiment

Pull Request - State: closed - Opened by singjc over 3 years ago
Labels: enhancement

#16 - Experiment: 50,000 Subsampled Reads

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: enhancement

#15 - [ADD] Upload moved changes of python notebooks:

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: enhancement

#14 - [UPDATE] Added Metaphlan and SRAdownload to snakemake pipeline

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: enhancement

#13 - Dev owen

Pull Request - State: closed - Opened by whitleyo almost 4 years ago

#12 - [ADD] Added Snakemake workflow to run pipeline

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: enhancement

#11 - [UPDATE] Added empty methods for metaphlan and export

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: enhancement

#10 - [FEATURE] Added command to run kneaddata

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: enhancement

#9 - [FEATURE] Randomly Subsample FASTQ Data using Seqtk

Pull Request - State: closed - Opened by singjc almost 4 years ago - 1 comment
Labels: enhancement

#8 - Pipeline Requirements

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

#7 - [ADD] Added document with ASCVD diagnostics screens and costs

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: documentation

#6 - [ADD] Added XGBoost, and simple Neural Network, included use of clinical data

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: enhancement

#5 - [UPDATE] Prediction on only 'ACVD', 'CRC', 'Crohns disease', 'Healthy'

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: enhancement

#4 - [ADD] Sequencing technology comparisons

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: documentation

#3 - [ADD] Added RF Feature Selection, tried nonlinear SVM and tried class…

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: enhancement

#2 - [ADD] One-vs-Rest Logistic Regression Classifier.

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: enhancement

#1 - [FEATURE] Added class frequency and confusion matrix plts

Pull Request - State: closed - Opened by singjc almost 4 years ago
Labels: enhancement