Ecosyste.ms: Issues

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GitHub / KevinMenden/scaden issues and pull requests

#130 - Aider

Pull Request - State: open - Opened by KevinMenden 3 months ago

#127 - Update scaden to work with Keras API

Pull Request - State: open - Opened by alex-d13 8 months ago

#125 - Scaden paper test data

Issue - State: open - Opened by jth3galv over 1 year ago - 1 comment

#123 - Illegal instruction on MacOS M1

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

#122 - IndexError: arrays used as indices must be of integer (or boolean) type

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

#121 - Scaden simulate, data input

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

#120 - some questions about ascites

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

#119 - some questions about ascites

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

#118 - ValueError: Input contains infinity or a value too large for dtype('float32').

Issue - State: open - Opened by chenjy327 about 3 years ago - 3 comments

#117 - Scaden web interface sign-in is down

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

#116 - Scaden process issue

Issue - State: open - Opened by ThomasThaewel over 3 years ago - 1 comment

#115 - About Scaden test

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

#114 - Merge mouse whole cell + infiltrating immune cell in cancer

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

#113 - ValueError: Input contains infinity or a value too large for dtype('float32').

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

#112 - ovarian cancer ascites sample

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

#111 - Preparing Count-matrix

Issue - State: open - Opened by bio-visualisation over 3 years ago

#110 - Scaden example command not found

Issue - State: closed - Opened by bio-visualisation over 3 years ago - 3 comments

#109 - Scaden simulate ValueError: low >= high

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

#108 - Error when using adata object

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

#107 - issues with conda version of scaden

Issue - State: closed - Opened by me37uday over 3 years ago - 3 comments

#104 - The simulated training dataset for the Human Brain.

Issue - State: closed - Opened by hathawayxxh over 3 years ago - 7 comments

#102 - execuse,I encounter some data issues

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

#101 - Timing scaden train on cpu vs gpu

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

#100 - Simulate errors out when celltype names are only numbers, requires text prefix to run correctly.

Issue - State: open - Opened by nagendraKU over 3 years ago - 1 comment
Labels: enhancement

#99 - PR for bugfix release 1.1.2

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

#98 - scaden train can't find key 'cell_types'

Issue - State: closed - Opened by sydneysue over 3 years ago - 8 comments

#97 - scaden process not running

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

#96 - singularity image or environment.yml

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

#95 - Pattern matching unintuitive

Issue - State: open - Opened by khkk378 over 3 years ago - 2 comments

#94 - Bug fix release v1.1.1

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

#92 - Scale model?

Issue - State: closed - Opened by khkk378 over 3 years ago - 1 comment

#91 - Experiments on real bulk data

Issue - State: closed - Opened by hathawayxxh over 3 years ago - 25 comments

#90 - Simulate slow

Issue - State: open - Opened by khkk378 over 3 years ago - 2 comments

#89 - Simulate distribution

Issue - State: closed - Opened by khkk378 over 3 years ago - 1 comment

#88 - M256 drop out rates in M1024

Issue - State: closed - Opened by khkk378 over 3 years ago - 2 comments

#87 - Pattern not matching in scaden simulate

Issue - State: closed - Opened by khkk378 over 3 years ago - 4 comments

#86 - Bump conda

Issue - State: closed - Opened by khkk378 over 3 years ago - 2 comments

#85 - Scaden example sometimes breaks

Issue - State: open - Opened by KevinMenden almost 4 years ago - 2 comments
Labels: bug

#84 - Release v1.1.0 PR

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

#83 - Curious about generating samples and labels from existing data

Issue - State: closed - Opened by PallaviSurana1 almost 4 years ago - 3 comments

#82 - Enable multiprocessing for data simulation

Issue - State: open - Opened by KevinMenden almost 4 years ago - 1 comment
Labels: enhancement

#81 - ADD h5ad input format option

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

#80 - Can you release the processed real bulk data for model validation?

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

#79 - PR for Scaden v1.0.2

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

#78 - Notify user if specified datasets are not part of the training data

Issue - State: closed - Opened by KevinMenden almost 4 years ago - 1 comment
Labels: enhancement

#77 - How to repeat the experiments in your paper

Issue - State: closed - Opened by hathawayxxh almost 4 years ago - 19 comments

#76 - Order of genes in prediction data

Issue - State: closed - Opened by amjass12 almost 4 years ago - 2 comments

#75 - Availability of sc-rnaseq data

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

#74 - Error when running simulate

Issue - State: closed - Opened by RK1912 almost 4 years ago - 17 comments

#73 - Normalization of the training expression data

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

#72 - "scaden example --out example_data/" doesn't work

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

#69 - Automatic cell type labeling for easier data preparation

Issue - State: open - Opened by KevinMenden about 4 years ago
Labels: enhancement

#68 - Memory footprint too big for simulation of large datasets

Issue - State: closed - Opened by KevinMenden about 4 years ago
Labels: enhancement

#67 - made dataset identification more robust

Pull Request - State: closed - Opened by KevinMenden about 4 years ago

#66 - Dataset recognition is not robust

Issue - State: closed - Opened by KevinMenden about 4 years ago - 1 comment
Labels: bug, priority

#65 - Scaden test

Issue - State: closed - Opened by Zhaohui-Ruan about 4 years ago - 1 comment
Labels: stale

#64 - About scaden simulate

Issue - State: closed - Opened by Zhaohui-Ruan about 4 years ago - 2 comments
Labels: enhancement

#63 - Data Scaden required

Issue - State: closed - Opened by Zhaohui-Ruan about 4 years ago - 9 comments

#62 - Error: fail to generate example data by using scaden expample

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

#61 - Version v1.0.0 release

Pull Request - State: closed - Opened by KevinMenden about 4 years ago

#60 - Problems with pattern finding in 'scaden simulate'

Issue - State: closed - Opened by KevinMenden about 4 years ago - 1 comment
Labels: bug

#59 - simulate and preprocess

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

#58 - mouse_brain.h5ad file

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

#57 - Update the documentation

Pull Request - State: closed - Opened by KevinMenden about 4 years ago

#56 - added GPU container building to action

Pull Request - State: closed - Opened by KevinMenden about 4 years ago

#55 - Configure GitHub actions to build docker images for CPU and GPU usage

Issue - State: closed - Opened by KevinMenden about 4 years ago - 1 comment
Labels: enhancement

#54 - fixed version badge

Pull Request - State: closed - Opened by KevinMenden about 4 years ago

#53 - Release 0.9.6

Pull Request - State: closed - Opened by KevinMenden about 4 years ago

#52 - Scaden simulate error: KeyError: 'Celltype'

Issue - State: closed - Opened by MarcusLCC about 4 years ago - 6 comments
Labels: help wanted

#51 - No 'simulate' command in docker image? And doc for h5da file content

Issue - State: closed - Opened by vdet about 4 years ago - 6 comments
Labels: question

#50 - Implement testing via GitHub actions

Issue - State: closed - Opened by KevinMenden about 4 years ago - 2 comments
Labels: enhancement

#49 - Version 0.9.5

Pull Request - State: closed - Opened by KevinMenden about 4 years ago

#48 - Make Scaden runs reproducible

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

#47 - Merge pull request #46 from KevinMenden/dev

Pull Request - State: closed - Opened by KevinMenden about 4 years ago

#46 - Syn Dev an Master branchs

Pull Request - State: closed - Opened by KevinMenden about 4 years ago

#45 - Refactor with TF 2.0

Issue - State: closed - Opened by KevinMenden about 4 years ago
Labels: enhancement, dependencies

#44 - Add lint function to inspect input files

Issue - State: closed - Opened by KevinMenden about 4 years ago - 1 comment
Labels: enhancement

#43 - PBMC2 (monaco) dataset in pbmc_data.h5ad

Issue - State: closed - Opened by mjjeon about 4 years ago - 4 comments
Labels: question

#42 - issues with the webtool

Issue - State: closed - Opened by liu-ying-jun about 4 years ago - 5 comments
Labels: enhancement

#41 - Replace deprecated as_matrix() with to_numpy()

Pull Request - State: closed - Opened by zeehio about 4 years ago

#40 - deprecated `as_matrix` in create_h5ad_file.py

Issue - State: closed - Opened by lucapandolfini over 4 years ago

#39 - Problem with Scaden process

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

#38 - Problem creating h5ad-file

Issue - State: closed - Opened by idalarsson over 4 years ago - 8 comments
Labels: bug

#37 - Is L1 loss function correct?

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

#36 - Bulk generation

Issue - State: closed - Opened by idalarsson over 4 years ago - 8 comments

#35 - Recommended #s for cells and # of samples

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

#34 - Normalization of input bulk data

Issue - State: closed - Opened by Tushar-87 over 4 years ago - 1 comment
Labels: question

#33 - predicting bulk RNA-seq

Issue - State: closed - Opened by Joliver3991 over 4 years ago - 2 comments

#32 - Consider adding the demo website?

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

#31 - Add script for Dockerfile auto-builds

Pull Request - State: closed - Opened by zeehio almost 5 years ago - 2 comments

#30 - tensorflow vs tensorflow-gpu

Issue - State: closed - Opened by zeehio almost 5 years ago - 3 comments

#29 - Add installation instructions

Pull Request - State: closed - Opened by zeehio almost 5 years ago - 1 comment

#28 - Fixed Dependency Problem - Version v0.9.4

Pull Request - State: closed - Opened by KevinMenden almost 5 years ago

#27 - Use anndata instead of scanpy

Pull Request - State: closed - Opened by zeehio almost 5 years ago