Ecosyste.ms: Issues

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

GitHub / lilab-bcb/pegasusio issues and pull requests

#115 - support parquet metadata format

Pull Request - State: open - Opened by yihming 18 days ago

#114 - Updated view copy code to remove unused categories

Pull Request - State: closed - Opened by bli25 6 months ago

#113 - Add support for Python 3.12

Pull Request - State: closed - Opened by yihming 8 months ago

#112 - Fail to install pegasusio

Issue - State: open - Opened by jiananwehi 9 months ago - 2 comments

#111 - UnimodalDataView.copy() returns MultimodalData by default

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

#110 - Fix Readthedocs

Pull Request - State: closed - Opened by yihming 11 months ago

#109 - Update CI test

Pull Request - State: closed - Opened by yihming 11 months ago

#108 - Decide the default matrix binding of the result by majority voting

Pull Request - State: closed - Opened by yihming 11 months ago

#107 - Added pop_matrix, update_matrix and as_int for matrix operations

Pull Request - State: closed - Opened by bli25 over 1 year ago

#106 - Don't raise exception if only one count matrix exists

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

#105 - Fixed a bug in UnimodalData

Pull Request - State: closed - Opened by bli25 over 1 year ago

#104 - Fixed a bug in zarr_utils for writing results

Pull Request - State: closed - Opened by bli25 over 1 year ago

#103 - Added function to remove quotes for read_csv function

Pull Request - State: closed - Opened by bli25 over 1 year ago

#102 - Added more suffices support for mtx file input

Pull Request - State: closed - Opened by bli25 almost 2 years ago

#101 - Convert np.object to object

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

#100 - AttributeError: module 'numpy' has no attribute 'object'

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

#99 - Fix issue on spatial coordinates

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

#98 - Partial fix for loading spaceranger v2 output

Pull Request - State: closed - Opened by bli25 about 2 years ago

#97 - Fixed bugs in Unimodal data to_anndata function:

Pull Request - State: closed - Opened by bli25 over 2 years ago

#96 - Modified loaded count matrix name from X to counts

Pull Request - State: closed - Opened by bli25 over 2 years ago

#95 - Added the option of adding UID in the constructor

Pull Request - State: closed - Opened by bli25 over 2 years ago

#94 - Added transpose option and fixed a bug in read_csv

Pull Request - State: closed - Opened by bli25 over 2 years ago

#93 - Fix issue with DropletUtils::read10xCount function in R

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

#92 - Added write to 10x h5

Pull Request - State: closed - Opened by bli25 over 2 years ago - 1 comment

#91 - Fixed a bug when upgrade zarr to 2.11.0

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

#90 - Bug fix for `MultimodalData.get_attr_type` function

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

#89 - Update qc_utils.py

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

#88 - initialize metadata before use

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

#87 - Formatting

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

#86 - Fix bug in write_dataframe of zarr_utils

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

#85 - Adjust filtering step for spatial data

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

#84 - Improve 10X Visium data loading

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

#83 - Updated for spatial analysis

Pull Request - State: closed - Opened by bli25 almost 3 years ago

#82 - Clean up Visium I/O code

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

#81 - spatial read and write to zarr

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

#80 - read/write spatial data to zarr

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

#79 - Rrocher

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

#78 - Fix issue on subclasses of UnimodalData

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

#77 - Fix issue on UnimodalData constructor

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

#76 - Resolve issue on QC

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

#75 - Avoid item assignment on NoneType object error

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

#74 - Added obsp and varp

Pull Request - State: closed - Opened by bli25 about 3 years ago

#73 - How to convert data.raw.X to anndata?

Issue - State: closed - Opened by Zifeng-L about 3 years ago - 4 comments

#72 - Fixed a bug for detecting correct NA values for bool series

Pull Request - State: closed - Opened by bli25 over 3 years ago

#71 - Fixed a bug in fill_na

Pull Request - State: closed - Opened by bli25 over 3 years ago

#70 - Add unit test for data aggregation

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

#69 - Enable sample-specific nUMI and nGene minimum threshold filtration

Pull Request - State: closed - Opened by bli25 over 3 years ago

#68 - Added support for composite list

Pull Request - State: closed - Opened by bli25 over 3 years ago

#67 - Fixed a bug removing uns entries

Pull Request - State: closed - Opened by bli25 over 3 years ago

#66 - Fixed bug

Pull Request - State: closed - Opened by bli25 over 3 years ago

#65 - make sure necessary categorical data are categorical again

Pull Request - State: closed - Opened by bli25 over 3 years ago

#64 - For merging data objects, use copy instead

Pull Request - State: closed - Opened by bli25 over 3 years ago

#63 - Added functionality to aggregate multimodal data objects

Pull Request - State: closed - Opened by bli25 over 3 years ago

#62 - Fix bug in previous fix of MultimodalData.subset_data() function

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

#61 - Fix bug for MultimodalData

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

#60 - Updated VDJdata

Pull Request - State: closed - Opened by bli25 over 3 years ago

#59 - reorg qc_utils and add pandas >=1.2.0

Pull Request - State: closed - Opened by bli25 over 3 years ago

#58 - Modified qc_utils to compute n_genes and n_counts anyway

Pull Request - State: closed - Opened by bli25 over 3 years ago

#57 - Fixed a critical bug prevent indexing using position arrays

Pull Request - State: closed - Opened by bli25 almost 4 years ago

#56 - update release notes

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

#55 - Resolve genome and modality naming; Update unit tests

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

#54 - Raise error message when detected unsupported output file name; also …

Pull Request - State: closed - Opened by bli25 almost 4 years ago

#53 - in a better format

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

#52 - Make genome and modality overwrite metadata if specified

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

#51 - UnimodalData constructor ignores explicit genome= and modality=

Issue - State: closed - Opened by LTLA almost 4 years ago - 8 comments

#50 - Fixed a bug for caching percent mito rate

Pull Request - State: closed - Opened by bli25 almost 4 years ago

#49 - Use cython fused types for sparse matrix outputs

Pull Request - State: closed - Opened by bli25 almost 4 years ago

#48 - Fix issue with qcviolin function in pegasus

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

#47 - Remove zero categories when using hashing or genetic pooling, modifie…

Pull Request - State: closed - Opened by bli25 almost 4 years ago

#46 - Adjust load_loom_file to work with Seurat-style

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

#45 - Fix bug on inconsistency of count matrix with feature info

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

#44 - Three updates. 1. do not recalculate n_genes, n_counts and percent_mi…

Pull Request - State: closed - Opened by bli25 about 4 years ago

#43 - Fixed a bug in loading mtx file

Pull Request - State: closed - Opened by bli25 about 4 years ago

#42 - Added get_genome in multimodal class

Pull Request - State: closed - Opened by bli25 about 4 years ago

#41 - Updated nanostring data and clean _tmp before writing out data objects

Pull Request - State: closed - Opened by bli25 about 4 years ago

#40 - Updated nanostring_utils

Pull Request - State: closed - Opened by bli25 about 4 years ago

#39 - Unable to Install Pegasus using pip3

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

#38 - Added support for Nanostring GeoMx data

Pull Request - State: closed - Opened by bli25 about 4 years ago

#37 - fix bug in generating SCP count matrix

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

#36 - Added cache_passqc

Pull Request - State: closed - Opened by bli25 about 4 years ago

#35 - Updated CITESeqData and CytoData to remove isotype subtraction

Pull Request - State: closed - Opened by bli25 about 4 years ago

#34 - Improved CiteSeq and Cyto datas

Pull Request - State: closed - Opened by bli25 over 4 years ago

#33 - Minor changes to work with Pegasus

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

#32 - Fixed a bug in loading mtx files

Pull Request - State: closed - Opened by bli25 over 4 years ago

#31 - Reformat shlex usage

Pull Request - State: closed - Opened by bli25 over 4 years ago

#30 - fix bug

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

#29 - use shlex.quote for filenames

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

#28 - Replacing genome names happens with --default-ref

Pull Request - State: closed - Opened by bli25 over 4 years ago

#27 - Convert added attributes into categorical and recognize nan for Refer…

Pull Request - State: closed - Opened by bli25 over 4 years ago

#26 - Modify dockerfile to enable unit test

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

#25 - reorg setup for linux wheel building

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

#24 - Updated mito

Pull Request - State: closed - Opened by bli25 over 4 years ago

#23 - Fixed another bug

Pull Request - State: closed - Opened by bli25 over 4 years ago

#22 - Updated

Pull Request - State: closed - Opened by bli25 over 4 years ago

#21 - Updated

Pull Request - State: closed - Opened by bli25 over 4 years ago

#20 - Add use_scm_version to setup.py

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

#19 - Updated

Pull Request - State: closed - Opened by bli25 over 4 years ago

#18 - clean up

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

#17 - Updated

Pull Request - State: closed - Opened by bli25 over 4 years ago

#16 - Sped up Data View

Pull Request - State: closed - Opened by bli25 over 4 years ago