Ecosyste.ms: Issues

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

GitHub / stemangiola/CuratedAtlasQueryR issues and pull requests

#151 - How to import dataset from collection?

Issue - State: open - Opened by YXC33 about 2 months ago - 7 comments

#150 - Import api with pseudobulk

Pull Request - State: open - Opened by myushen 2 months ago

#149 - could not run pseudobulk on imported data

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

#148 - solve corrupted pseudobulk assays

Pull Request - State: closed - Opened by myushen 3 months ago

#147 - add reference to exported functions

Pull Request - State: closed - Opened by myushen 4 months ago

#144 - cache for pseudobulk same as for single cell?

Issue - State: open - Opened by stemangiola 4 months ago - 1 comment

#143 - update validation columns for get_sce

Pull Request - State: closed - Opened by myushen 4 months ago - 3 comments

#142 - add citation

Pull Request - State: closed - Opened by myushen 5 months ago - 1 comment

#141 - Add citation file

Issue - State: open - Opened by stemangiola 5 months ago

#140 - fix multiple cell ids match with the same dataset id

Pull Request - State: closed - Opened by myushen 5 months ago

#139 - update testthat

Pull Request - State: closed - Opened by myushen 5 months ago

#138 - fix parquet pattern

Pull Request - State: closed - Opened by myushen 5 months ago

#137 - Get pseudobulk api

Pull Request - State: closed - Opened by myushen 6 months ago - 7 comments

#136 - add get_pseudobulk API

Issue - State: open - Opened by stemangiola 6 months ago - 4 comments

#135 - import api

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

#134 - import api

Pull Request - State: closed - Opened by myushen 7 months ago

#133 - Import metadata, counts api

Pull Request - State: closed - Opened by myushen 7 months ago

#131 - metadata accepts multiple databases

Pull Request - State: closed - Opened by myushen 7 months ago - 4 comments

#130 - update metadata function to allow interacting multiple databases

Pull Request - State: closed - Opened by myushen 8 months ago - 1 comment

#129 - Improve get_metadata() docs

Pull Request - State: closed - Opened by multimeric 8 months ago - 2 comments

#128 - Referenced table not found!

Issue - State: closed - Opened by stemangiola 9 months ago

#128 - Referenced table not found!

Issue - State: closed - Opened by stemangiola 9 months ago

#127 - DelayedMatrix not Sparse?

Issue - State: closed - Opened by stemangiola 9 months ago - 2 comments

#125 - Trying to use the package: accessing the METADATA_URL

Issue - State: open - Opened by shivUSF 9 months ago - 1 comment

#124 - file_id_db=="e427efe71e8e94de5b3e48eb98236323" fails

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

#124 - file_id_db=="e427efe71e8e94de5b3e48eb98236323" fails

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

#123 - duplicate 'row.names' are not allowed

Issue - State: open - Opened by stemangiola 9 months ago - 6 comments

#122 - Fix "Binder Error: Referenced table not found!"

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

#119 - how to cite this work ?

Issue - State: closed - Opened by Lin-Yux 12 months ago - 2 comments

#118 - Post Submission Fixes

Pull Request - State: closed - Opened by multimeric 12 months ago

#117 - Enable use_cache = FALSE for get_metadata()

Pull Request - State: open - Opened by krlong68 12 months ago - 2 comments

#115 - Pin Matrix version

Pull Request - State: closed - Opened by multimeric about 1 year ago

#114 - Method consistency

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

#113 - Error when downloading cell data while using Linux / SLURM / HPC

Issue - State: closed - Opened by william-hutchison over 1 year ago - 5 comments

#112 - Improve figures

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

#111 - Allow h5 seurat for anndata

Pull Request - State: closed - Opened by stemangiola over 1 year ago - 3 comments

#110 - One vignette

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

#109 - Bioc review changes

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

#108 - Update counts version to 0.2.1

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

#107 - Missing cell message

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

#106 - correct typo in tissue harmonised

Issue - State: open - Opened by stemangiola over 1 year ago

#105 - Add dir_to_anndata function

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

#104 - Some studies of the Human Cell Atlas cannot be found

Issue - State: open - Opened by KoppyTheKid over 1 year ago - 3 comments

#103 - Bioc improvements

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

#102 - Download size reporting

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

#101 - submit the package to Bioconductor

Issue - State: closed - Opened by stemangiola over 1 year ago - 2 comments

#100 - Cache connection

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

#99 - Implementation of the new suggested unharmonised API

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

#98 - Update readme

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

#97 - Add support for unharmonised metadata

Pull Request - State: closed - Opened by multimeric over 1 year ago - 14 comments

#96 - Create `update_database()` for updating metadata

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

#95 - "Author Categories" accessible?

Issue - State: closed - Opened by jgilis over 1 year ago - 4 comments
Labels: enhancement

#94 - update README

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

#93 - No cpm by default

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

#92 - querying counts by default

Issue - State: closed - Opened by stemangiola over 1 year ago

#91 - README inconsistencies - Visualise gene Transcription section

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

#90 - Minor repo/website feedback

Issue - State: open - Opened by multimeric over 1 year ago - 5 comments

#89 - drop library()

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

#87 - Remove `library()` call from vignette/readme

Issue - State: closed - Opened by multimeric over 1 year ago

#86 - update code

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

#85 - plan forward

Issue - State: open - Opened by stemangiola over 1 year ago

#83 - Fix 78

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

#82 - Different row numbers

Issue - State: closed - Opened by multimeric over 1 year ago - 3 comments

#81 - fix images

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

#80 - change to cell_

Pull Request - State: closed - Opened by stemangiola over 1 year ago - 4 comments

#79 - Fix "Column `output_dir` not found in `.data`"

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

#78 - `_cell` must be size 202 or 1, not 157.

Issue - State: closed - Opened by stemangiola over 1 year ago - 10 comments

#77 - update docs and README

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

#76 - R CMD check

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

#75 - Update db to 0.2

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

#74 - Database update process

Issue - State: open - Opened by multimeric over 1 year ago - 3 comments

#73 - Update readme

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

#72 - Fix 65

Pull Request - State: closed - Opened by multimeric over 1 year ago - 2 comments

#71 - [EDIT] whole DB preview slower in Rstudio HPC than local Rstudio

Issue - State: closed - Opened by stemangiola over 1 year ago - 3 comments

#70 - Track used access for metadata query and file download

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

#69 - Separate the HCA content from this API repository

Issue - State: open - Opened by stemangiola over 1 year ago

#68 - Fix #66

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

#67 - Error while installing package

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

#66 - get_metadata() alone give no output

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

#65 - minor bugs/improvements

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

#64 - Update get_SingleCellExperiment(assays) documentation

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

#63 - Reuse connection

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

#62 - Use duckdb instead of sqlite

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

#61 - Documentation inconsistent?

Issue - State: closed - Opened by vjcitn over 1 year ago

#60 - Prepare users for 36GB download

Issue - State: closed - Opened by vjcitn over 1 year ago - 17 comments

#59 - Documentation

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

#58 - R CMD check

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

#57 - Update DB to version 0.2 for counts, and 0.2.1 for metadata

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

#56 - decrease DB size, through a permanent VIEW?

Issue - State: closed - Opened by stemangiola over 1 year ago - 7 comments

#55 - Create GIF video for the API usage

Issue - State: open - Opened by stemangiola over 1 year ago

#54 - Fix github actions

Issue - State: closed - Opened by stemangiola over 1 year ago - 5 comments