nvidia-genomics-research/rapids-single-cell-examples issues and pull requests

#121 - Leiden CLustering takes too long

Issue - State: open - Opened by siddharthamantrala 3 months ago

#120 - weird UMAP results and very inconsistent with CPU results

Issue - State: open - Opened by yubin-ai 10 months ago - 1 comment

#119 - cell number limit: data point for 10M and 70M dataset

Issue - State: open - Opened by yubin-ai about 1 year ago

#118 - gpu memory issue - 8M cell 24G GPU out of memory during umap

Issue - State: open - Opened by yubin-ai about 1 year ago - 1 comment

#117 - change of cuml library

Issue - State: open - Opened by yubin-ai about 1 year ago

#116 - Illegal Memory Access: 1.3M cells RTX A6000 48GB out of memory on scaling step

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

#115 - ImportError: /usr/lib/x86_64-linux-gnu/libcuda.so.1: file too short

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

#114 - Updating coverage.py

Pull Request - State: closed - Opened by cjnolet almost 2 years ago

#113 - Updating conda to pull from my rapidgenomics fork

Pull Request - State: closed - Opened by cjnolet almost 2 years ago

#112 - iUpdating dockerfile

Pull Request - State: closed - Opened by cjnolet almost 2 years ago

#111 - fix `rapids_scanpy_funcs.highly_variable_genes`

Issue - State: open - Opened by hw-ju almost 2 years ago

#110 - can't run inference with atacworks pretrained model within the container on A100

Issue - State: open - Opened by hw-ju almost 2 years ago

#109 - jupyter notebooks difference between in the repo and within docker container

Issue - State: open - Opened by hw-ju almost 2 years ago

#108 - TypeError: rank_genes_groups() got multiple values for argument 'groups'

Issue - State: open - Opened by archieandrews10 almost 2 years ago

#107 - rank_gene_group_fix for rapids-23.02

Pull Request - State: closed - Opened by Intron7 almost 2 years ago

#106 - Adding zenodo DOI

Pull Request - State: closed - Opened by cjnolet almost 2 years ago

#105 - updated and fixed rank_gene_groups

Pull Request - State: closed - Opened by Intron7 almost 2 years ago - 1 comment

#104 - scanpy_funcs: Use multi-target regression

Pull Request - State: closed - Opened by ahendriksen almost 2 years ago - 14 comments

#103 - Cannot open UCX library: (null) in PCA analysis of 1M_brain_gpu_analysis_multigpu

Issue - State: open - Opened by ChenPeizhan about 2 years ago - 3 comments

#102 - error of read_with_filter function

Issue - State: open - Opened by 111kakaluote about 2 years ago

#101 - The results consistency of RAPIDS implementation

Issue - State: open - Opened by 111kakaluote about 2 years ago

#100 - RuntimeError: exception occured! when analysis using multigpu

Issue - State: open - Opened by 111kakaluote about 2 years ago - 2 comments

#99 - MultiGPU notebooks calculated differentially expressed PCAs

Issue - State: closed - Opened by Intron7 about 2 years ago - 1 comment

#98 - Updating for rapids 22.08

Pull Request - State: closed - Opened by cjnolet about 2 years ago - 1 comment

#97 - error in rapids_scanpy_funcs.highly_variable_genes

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

#96 - Residual GPU Memory usage

Issue - State: open - Opened by r614 about 2 years ago - 3 comments

#95 - Getting a scalar from an IntervalIndex is not yet supported

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

#94 - csr_matrix with the .get method will return "Last value of index pointer should be less than the size of index and data arrays"

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

#93 - conda import environment not working

Issue - State: open - Opened by tnnandi over 2 years ago - 1 comment

#92 - update citation to preprint

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

#91 - Updating dockerfile for 22.02

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

#90 - Updates for RAPIDS 22.02 and scanpy 1.9.1

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

#89 - rapids for pyscenic

Issue - State: open - Opened by Wulin-Tan over 2 years ago

#88 - Fix preprocess batch

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

#87 - Bug in preprocess_in_batches

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

#86 - rank_genes_groups fix

Pull Request - State: closed - Opened by Intron7 almost 3 years ago - 2 comments

#85 - Update rapids 21.12

Pull Request - State: closed - Opened by Intron7 almost 3 years ago

#84 - Updates for rapids 21.12

Pull Request - State: closed - Opened by cjnolet almost 3 years ago - 9 comments

#83 - [REVIEW] Using multi-gpu PCA, kmeans, and UMAP

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

#82 - [REVIEW] Multi gpu

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

#81 - Change to scripts for upgrading to RAPIDS 2021.08...

Pull Request - State: closed - Opened by rilango about 3 years ago - 2 comments

#80 - Adding branch modified for dataproc users [DO NOT MERGE]

Pull Request - State: closed - Opened by bradmiro over 3 years ago - 1 comment

#79 - 21.06 upgrade + benchmarks

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

#78 - Updating notebooks and conda environments for RAPIDS release 21.08

Pull Request - State: closed - Opened by cjnolet over 3 years ago - 5 comments

#77 - Alal/single gpu batching

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

#76 - Update rapids_scanpy_funcs.py to work with new scanpy version and rapids-0.19

Pull Request - State: closed - Opened by Intron7 over 3 years ago

#75 - Batched preprocessing for 1M cell notebook...

Pull Request - State: closed - Opened by rilango over 3 years ago - 5 comments

#74 - added new features and functionalities

Pull Request - State: closed - Opened by Intron7 over 3 years ago - 2 comments

#73 - CUDARuntimeError in Notebooks

Issue - State: closed - Opened by Intron7 over 3 years ago - 15 comments

#72 - Nearest neighbors graph computation crashes

Issue - State: open - Opened by manock over 3 years ago - 1 comment
Labels: bug

#71 - Added Resolution for Leiden Function

Pull Request - State: closed - Opened by Intron7 over 3 years ago

#70 - minor updates to notebook text

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

#69 - Bugfix: Visualization tool is not accessible from remote machine over http…

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

#69 - Bugfix: Visualization tool is not accessible from remote machine over http…

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

#68 - Change container version

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

#67 - Upgrade to Rapids 0.17

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

#66 - new benchmarks

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

#65 - updated 1M notebooks for benchmarking

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

#64 - Update description

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

#63 - A new script to replace launch.sh...

Pull Request - State: closed - Opened by rilango almost 4 years ago - 1 comment

#62 - Add atacworks as a dependency

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

#61 - Fix conda env creation issue...

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

#60 - Add multicore-tsne python package.

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

#59 - 015 updates

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

#58 - Reverting back to rapids0.15

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

#57 - reverting to 3f02571

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

#56 - updated calls to rapids 0.16

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

#55 - fixed timer in atacworks notebook

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

#54 - [BUG] Many of cuML's models that use cublas/cusolver/cusparse are limited in the number of cells that can be processed

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

#53 - [FEA] Add batching option to `filter_cells` and `filter_genes` in `rapids_scanpy_funcs`

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

#52 - added atac reqs to conda files

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

#51 - AtacWorks notebook GPU version

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

#50 - OverflowError: value too large to convert to int

Issue - State: open - Opened by slowkow about 4 years ago - 2 comments

#49 - Adding benchmark results for a100

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

#48 - A new script to replace launch.sh and fix for issues in viz...

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

#47 - Launch script for starting notebooks in a conda env or container...

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

#41 - CUDA MemoryError for loading adata variable names to cudf.Series method

Issue - State: open - Opened by nullbyte91 about 4 years ago - 3 comments

#40 - Cleanup docker file...

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

#39 - Docker container with all dependency build for the notebook...

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

#38 - Rapids 0.15 upgrade

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