Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / NVIDIA-Genomics-Research/AtacWorks issues and pull requests

#252 - Removing batch bias

Issue - State: open - Opened by liqing9102 7 months ago

#251 - Error: `torch.cuda.OutOfMemoryError: CUDA out of memory`

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

#248 - Error running atacworks train

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

#247 - Tutorial 1 is recursive?

Issue - State: open - Opened by albertdyu almost 3 years ago - 1 comment

#246 - ConnectionResetError: [Errno 104] Connection reset by peer

Issue - State: open - Opened by hhvu0102 about 3 years ago

#245 - Removing hard-set versions from requirements.txt to be more compatible with RAPIDS

Pull Request - State: open - Opened by cjnolet over 3 years ago - 2 comments

#244 - error message needing help

Issue - State: open - Opened by elffairy90 over 3 years ago - 1 comment

#243 - mouse reference genome

Issue - State: closed - Opened by elffairy90 over 3 years ago - 1 comment

#242 - [gpuCI] Forward-merge master to dev-v0.4.0

Pull Request - State: open - Opened by GPUtester over 3 years ago - 1 comment

#241 - Update Requirements.txt - master branch

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

#240 - Update dependencies

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

#239 - mouse reference

Issue - State: closed - Opened by elffairy90 over 3 years ago - 2 comments

#238 - Update requirements.txt

Pull Request - State: closed - Opened by ntadimeti over 3 years ago - 2 comments

#237 - Atacworks stuck at "waiting for writter to finish..."

Issue - State: open - Opened by rochevin almost 4 years ago - 3 comments

#236 - Pretrained model for bulk low-quality data

Issue - State: open - Opened by avantikalal almost 4 years ago - 6 comments

#235 - What does the 6 kb mean?

Issue - State: open - Opened by YichaoOU almost 4 years ago - 3 comments

#234 - Update citation

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

#233 - error in pip install -r requirments.txt

Issue - State: open - Opened by elffairy90 almost 4 years ago - 1 comment

#232 - Error when passing directories for training

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

#231 - WIP: Enable reading config files output by atacworks

Pull Request - State: open - Opened by ntadimeti about 4 years ago - 1 comment

#230 - WIP: Combine tile functions in utils.py

Pull Request - State: closed - Opened by ntadimeti about 4 years ago - 1 comment

#229 - Sort the files in dir to ensure paired readings

Pull Request - State: closed - Opened by ntadimeti about 4 years ago - 1 comment

#228 - name h5 file based on noisybw instead of cleanbw

Pull Request - State: closed - Opened by ntadimeti about 4 years ago - 3 comments

#227 - WIP: Update versions of all dependencies

Pull Request - State: open - Opened by ntadimeti about 4 years ago - 1 comment

#226 - Update scikit-learn version

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

#225 - Update atacworks dependencies to scikit-learn 0.23.2

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

#224 - Add rapids atacworks example

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

#223 - Update atacworks dependencies to latest stable versions

Issue - State: open - Opened by ntadimeti about 4 years ago

#222 - Update documentation

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#221 - AtacWorks errors on custom data

Issue - State: closed - Opened by asundaresan1 over 4 years ago - 15 comments

#220 - [gpuCI] Auto-merge master to dev-v0.4.0 [skip ci]

Pull Request - State: closed - Opened by GPUtester over 4 years ago - 1 comment

#219 - Soften the requirements

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#218 - Add compatibility version specifier

Pull Request - State: closed - Opened by ntadimeti over 4 years ago - 1 comment

#217 - h5 file naming

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

#216 - files not read in sorted order

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

#215 - fix evaluation

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#214 - Fix batch size arg

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#213 - Version promotion scripts for automatic release job

Pull Request - State: closed - Opened by ohadmo over 4 years ago

#212 - atacworks inference getting stuck at writing stage

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

#211 - scanpy installation conflicts with atacworks

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

#210 - Fix release version

Pull Request - State: closed - Opened by ntadimeti over 4 years ago - 2 comments

#209 - Add unit tests for data loader

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

#208 - Fix train dataloader

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#207 - In training, same sample is being stored per batch.

Issue - State: closed - Opened by ntadimeti over 4 years ago
Labels: bug

#206 - Update defaults

Pull Request - State: closed - Opened by avantikalal over 4 years ago

#205 - Add new docker instructions

Pull Request - State: closed - Opened by ntadimeti over 4 years ago - 3 comments

#204 - Fix wheel package location

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#203 - Merge dev-v0.3.0 to master

Pull Request - State: closed - Opened by ntadimeti over 4 years ago - 1 comment

#202 - Update final details

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#201 - Add interactive docker command

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#200 - SA review

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#197 - combine tile_interval functions in utils.py

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

#196 - Update tutorial notebooks

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#195 - Trying to pip install on a cluster

Issue - State: closed - Opened by hugokitano over 4 years ago - 53 comments

#194 - Add support to read h5 files

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#193 - Cleaning up docs

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#192 - Add advanced section in documentation

Pull Request - State: closed - Opened by ntadimeti over 4 years ago - 1 comment

#191 - Add otuput resolution

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#190 - write binned

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#189 - Add regions flag

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#188 - tutorial2: Inference output data

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

#187 - Remove unncessary args

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#186 - Revert "Alal/write binned"

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#185 - Add unit testing for bigwigio.py and bedgraphio.py

Pull Request - State: closed - Opened by rmovva over 4 years ago - 1 comment

#184 - Convert scripts to modules

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#183 - Encode intervals, sizes data into h5 files itself.

Issue - State: open - Opened by ntadimeti over 4 years ago
Labels: enhancement

#182 - Add unit testing for bedio.py and h5io.py

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#181 - WIP: Remove individual scripts and modularize the pre-processing steps

Pull Request - State: closed - Opened by ntadimeti over 4 years ago - 3 comments

#180 - [CI] Add local prebuild script

Pull Request - State: closed - Opened by ohadmo over 4 years ago

#179 - PYPI installation script

Pull Request - State: closed - Opened by ntadimeti over 4 years ago - 4 comments

#178 - Alal/write binned

Pull Request - State: closed - Opened by avantikalal over 4 years ago - 1 comment

#177 - Change --gpu to --gpu_id to clarify the functionality

Pull Request - State: closed - Opened by ntadimeti over 4 years ago - 3 comments

#176 - Update documentation, point to jupyter notebooks

Pull Request - State: closed - Opened by ntadimeti over 4 years ago

#175 - Trying Atacworks on custom data

Issue - State: closed - Opened by ntadimeti over 4 years ago - 10 comments

#174 - CI scripts cleanup

Pull Request - State: closed - Opened by ohadmo over 4 years ago - 2 comments

#173 - Update documentation

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

#172 - Add entry point script to atacworks

Pull Request - State: closed - Opened by ntadimeti over 4 years ago - 1 comment

#171 - Alal/docs

Pull Request - State: closed - Opened by avantikalal over 4 years ago - 2 comments

#170 - Add set of standard config files

Issue - State: open - Opened by avantikalal over 4 years ago

#169 - Input/output binned data

Issue - State: closed - Opened by avantikalal over 4 years ago
Labels: enhancement

#168 - replace gpu: None with a more intuitive config option

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

#167 - Jupyter notebooks for tutorials

Pull Request - State: closed - Opened by ntadimeti over 4 years ago - 9 comments

#166 - invalid_crossdevice_link

Pull Request - State: closed - Opened by ntadimeti over 4 years ago - 1 comment

#163 - Create pre-trained model registry on NGC

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

#162 - AWS AMI

Issue - State: open - Opened by ntadimeti over 4 years ago
Labels: enhancement

#161 - Sphynx documentation

Issue - State: closed - Opened by ntadimeti over 4 years ago - 2 comments
Labels: documentation

#160 - Move tutorials into jupyter notebook format from md files.

Issue - State: closed - Opened by ntadimeti over 4 years ago - 2 comments
Labels: enhancement

#159 - enable automated docker image upload with new merges to master

Issue - State: open - Opened by ntadimeti over 4 years ago - 1 comment
Labels: enhancement

#156 - Remove pre-processing scripts and call them as modules in main script.

Issue - State: closed - Opened by ntadimeti almost 5 years ago - 1 comment
Labels: enhancement

#154 - updated output folder name in tutorial 1

Pull Request - State: closed - Opened by avantikalal almost 5 years ago - 3 comments

#153 - main.py infer: error: argument --gpu: invalid int value: 'None'

Issue - State: closed - Opened by feefee20 almost 5 years ago - 51 comments
Labels: bug, question

#152 - Update command line options and tutorials

Pull Request - State: closed - Opened by ntadimeti almost 5 years ago - 3 comments

#151 - added pretrained models list

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

#141 - Prefetch layers in inference to avoid OOM issues

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

#122 - package and upload atacworks to PyPi

Issue - State: closed - Opened by ntadimeti about 5 years ago - 2 comments
Labels: enhancement

#114 - Fix to include ends of chromosomes.

Issue - State: open - Opened by avantikalal about 5 years ago - 2 comments
Labels: bug