labsyspharm/scimap issues and pull requests

#125 - BrokenProcessPool: A task has failed to un-serialize. Please ensure that the arguments of the function are all picklable.

Issue - State: open - Opened by rohandavidg about 1 month ago

#124 - ValueError: Expected 2D array, got 1D array instead for rescale after manual gating

Issue - State: closed - Opened by rach-crc 2 months ago - 4 comments

#123 - Building neighborhoods

Issue - State: open - Opened by andreevg04 3 months ago - 1 comment

#122 - fix subset bug in addROI_image.py

Pull Request - State: closed - Opened by SarkkinenJ 3 months ago - 2 comments

#121 - %gui qt did not work and napari window did not pop up

Issue - State: closed - Opened by rach-crc 3 months ago - 4 comments

#120 - ValueError expecting 2D array at `sm.pp.rescale()` step

Issue - State: closed - Opened by sobjb7osx2 3 months ago - 3 comments

#119 - CODEX dataset with 200 images

Issue - State: open - Opened by andreevg04 4 months ago - 4 comments

#118 - feat: adding conda package build recipe

Pull Request - State: closed - Opened by ruiheesi 4 months ago - 1 comment

#117 - spatial_interaction - issues with rare cell type handling

Issue - State: open - Opened by gesavoigt 4 months ago

#116 - Using SCIMAP with MERFISH or Visium data

Issue - State: open - Opened by poloarol 5 months ago - 1 comment

#115 - return_data not working for plots

Issue - State: open - Opened by LukasHats 5 months ago - 1 comment

#113 - spatial interaction z scores

Issue - State: open - Opened by YuanningEric 6 months ago

#112 - kernel keep dying

Issue - State: open - Opened by jianxinwang 6 months ago - 3 comments

#111 - Implicit change in matplotlib parameters while importing scimap

Issue - State: closed - Opened by ConstensouxAlexis 7 months ago - 3 comments

#110 - Inquiry on Handling Imbalanced CODEX Data for Cellular Neighborhood Calculations in Scimap

Issue - State: open - Opened by Yuchen588 7 months ago - 5 comments

#109 - Fixed str dtype for Unknown cells, Closes #107

Pull Request - State: closed - Opened by emmanuel-contreras 7 months ago - 1 comment

#108 - overlapping legend on sm.pl.heatmap when constrained_layout set to True, and default arguments

Issue - State: closed - Opened by emmanuel-contreras 7 months ago - 6 comments

#107 - TypeError: Feature names are only supported if all input features have string names, but your input has ['str', 'str_'] when running sm.tl.spatial_cluster

Issue - State: closed - Opened by emmanuel-contreras 7 months ago - 1 comment

#106 - sm.pp.rescale and sm.tl.phenotype for phenotyping not adhering to user-dfined gates

Issue - State: closed - Opened by LukasHats 8 months ago - 6 comments

#105 - Gating QC plots no longer implemented in scimap.pp.rescale()

Issue - State: open - Opened by CameronFRWatson 9 months ago

#104 - Minor edits to paper

Pull Request - State: closed - Opened by csoneson 9 months ago

#103 - Update classify.py

Pull Request - State: closed - Opened by sarafiller 9 months ago - 1 comment

#102 - spatial_lda reproducibility

Issue - State: open - Opened by batukav 10 months ago

#101 - Package test coverage

Issue - State: closed - Opened by jluethi 10 months ago - 7 comments

#100 - How do I run the tests?

Issue - State: closed - Opened by kevinyamauchi 10 months ago - 4 comments

#99 - "command not found: pipx" when setting up development environment

Issue - State: closed - Opened by kevinyamauchi 10 months ago - 2 comments

#98 - .vscode in the repo

Issue - State: closed - Opened by kevinyamauchi 10 months ago - 2 comments

#97 - upgrade the latest version

Issue - State: closed - Opened by yas92 11 months ago - 3 comments

#96 - Bug in PIP INSTALL SCIMAP

Issue - State: closed - Opened by virlyananda 11 months ago - 21 comments

#95 - Fixed _classify.py bugs

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

#94 - Bump black from 19.10b0 to 24.3.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies

#93 - Napari doesnt open and code crashes.

Issue - State: closed - Opened by andreevg04 12 months ago - 5 comments

#92 - np.warnings.filterwarnings('ignore') no longer supported by numpy

Issue - State: closed - Opened by milesbailey121 about 1 year ago - 3 comments

#91 - Numpy ArrayMemoryError

Issue - State: closed - Opened by lukezhang-811 about 1 year ago - 1 comment

#90 - Bump aiohttp from 3.9.0 to 3.9.2

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#89 - Bump aiohttp from 3.8.6 to 3.9.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#88 - Interpretibility of adata.uns['spatial_interaction']

Issue - State: open - Opened by Dillon214 about 1 year ago - 1 comment

#87 - Bump pillow from 10.1.0 to 10.2.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#86 - Bump jinja2 from 3.1.2 to 3.1.3

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#85 - batch samples analysis

Issue - State: open - Opened by yas92 about 1 year ago - 3 comments

#84 - Apply MIT license

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

#83 - adata.raw.X vs. adata.X

Issue - State: closed - Opened by josenimo about 1 year ago - 1 comment

#82 - %gui qt not running (M2)

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

#81 - Added functionality to sm.hl.classify()

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

#80 - Added functionality to classify helper function

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

#79 - Napari automatically downsamples image when using sm.pl.gate_finder()

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

#78 - Bump urllib3 from 1.26.15 to 1.26.18

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#77 - Bump urllib3 from 1.26.15 to 1.26.17

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#76 - Installation problem on Mac

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

#75 - How can I get the test p value of two groups when comparing the distances between two cell types

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

#74 - Wrong figure in the "Getting Started with Scimap" tutorial

Issue - State: closed - Opened by ziyuanzhao2000 over 1 year ago - 1 comment

#73 - not maching gating area with the image

Issue - State: open - Opened by Elena983 over 1 year ago - 1 comment

#72 - Can I gate .qptiff image?

Issue - State: open - Opened by xyin0918 over 1 year ago - 1 comment

#71 - spatial_lda and recurrent cellular neighborhoods

Issue - State: open - Opened by batukav over 1 year ago - 4 comments

#70 - how to export the particular data file about the distance calculation

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

#69 - mcmicro_to_scimap add a condition to error out if multiple dim CSV files are provided

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

#68 - Bump certifi from 2022.12.7 to 2023.7.22

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#67 - Bump aiohttp from 3.8.4 to 3.8.5

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#66 - Add spatial obsm to adata on MCMICRO loading

Pull Request - State: open - Opened by adamjtaylor over 1 year ago

#65 - attempt to fix failed checks

Pull Request - State: open - Opened by amorje over 1 year ago