Ecosyste.ms: Issues

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GitHub / BiomedicalMachineLearning/stLearn issues and pull requests

#314 - Import H&E Image for Xenium

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

#313 - ValueError in stlearn.Read10X step

Issue - State: open - Opened by TLC199676 about 2 months ago

#312 - Cell to cell interaction: required data

Issue - State: open - Opened by JestlinNg 2 months ago

#311 - Import issue

Issue - State: open - Opened by elmir-ma 2 months ago

#309 - CCI Maps might have reversed axis labels!

Issue - State: open - Opened by je71xusa 4 months ago - 1 comment

#308 - Having trouble understanding the cell cell interaction table

Issue - State: closed - Opened by QiuYue117 4 months ago - 1 comment

#307 - Error when running st.pl.cluster_plot

Issue - State: open - Opened by kevin198930 4 months ago

#306 - Running time of PTST analysis for Xenium data

Issue - State: open - Opened by Ferris01 4 months ago

#304 - Gridding visualization with h&e image out of frame

Issue - State: open - Opened by Rabitta99 5 months ago

#301 - visium HD application

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

#299 - Clarification on Directionality in stLearn CCI Plots

Issue - State: open - Opened by gity123987 5 months ago - 2 comments

#297 - label_transfer_bc.csv

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

#296 - using stlearn for the first time.

Issue - State: open - Opened by oabuhuss 6 months ago - 1 comment

#295 - Run stSME clustering without HE

Issue - State: closed - Opened by rocketeer1998 6 months ago - 3 comments

#293 - Installation issue with version conflicts

Issue - State: open - Opened by Huyuling1 6 months ago - 5 comments

#292 - update dependency

Pull Request - State: closed - Opened by xiao233333 6 months ago

#291 - Installation issues on linux machine

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

#290 - module 'numpy' has no attribute 'int'.

Issue - State: closed - Opened by Rafael-Silva-Oliveira 8 months ago - 1 comment

#289 - fix: fix several bugs of CCI and zoom

Pull Request - State: closed - Opened by duypham2108 8 months ago

#288 - How does stlearn calculates the number of L-R pairs of celltype

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

#287 - 【bug】 code error

Issue - State: closed - Opened by lvmt 9 months ago - 1 comment

#286 - Question about st.spatial.trajectory.compare_transitions

Issue - State: open - Opened by zyy23 9 months ago - 1 comment

#285 - Is it possible to run CCI in muti-sample?

Issue - State: closed - Opened by yunbokai 9 months ago - 1 comment

#282 - Trajectory Zoom

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

#280 - Single cell transcriptomic data for cell-cell communication

Issue - State: closed - Opened by liangbolyu 10 months ago - 3 comments

#279 - Could not control the root in the trajectory

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

#278 - Installation issue on Mac M3

Issue - State: open - Opened by earn97 11 months ago - 3 comments

#277 - Issue loading stlearn

Issue - State: closed - Opened by KarlKaise 11 months ago - 1 comment

#276 - stlearn attributes not found

Issue - State: closed - Opened by mvereten 11 months ago - 1 comment

#275 - error when using st.spatial.trajectory.pseudotimespace_local

Issue - State: closed - Opened by cynthier 11 months ago - 2 comments

#273 - fix: fix current issues

Pull Request - State: closed - Opened by duypham2108 11 months ago

#272 - question for st.pl.cluster_plot fuction

Issue - State: closed - Opened by sycdegh 11 months ago - 2 comments

#271 - Question on create_stlearn function

Issue - State: closed - Opened by cxlpanpan 11 months ago - 2 comments

#270 - stlearn CCI is not working for multiple slides?

Issue - State: closed - Opened by howtofindme 11 months ago - 2 comments

#268 - Pseudo-time-space analysis problem

Issue - State: closed - Opened by PIGAsHIT 12 months ago - 8 comments

#267 - st.ReadXenium issue

Issue - State: closed - Opened by yandouwahhh about 1 year ago - 2 comments

#266 - How to get clear cell-pairs and ligand-receptor？

Issue - State: closed - Opened by Knight1995 about 1 year ago - 3 comments

#265 - st.tl.cci.run "AttributeError: module 'numpy' has no attribute 'int'."

Issue - State: closed - Opened by skim245 about 1 year ago - 2 comments

#264 - ValueError in step 2 of CCI analysis

Issue - State: closed - Opened by Rachel-qianqian about 1 year ago - 2 comments

#263 - Question about CCI distance

Issue - State: closed - Opened by Knight1995 about 1 year ago

#262 - save anndata object to h5ad file

Issue - State: closed - Opened by rialc13 about 1 year ago - 2 comments

#261 - How to get the clade no.s after generating trajectory plot

Issue - State: closed - Opened by rialc13 about 1 year ago - 3 comments

#260 - Is pseudoroot & iroot the same?

Issue - State: closed - Opened by rialc13 about 1 year ago - 1 comment

#259 - How to add my own LR pair?

Issue - State: closed - Opened by Knight1995 about 1 year ago - 4 comments

#257 - Allow saving tiles as PNG images in `stlearn.pp.tiling`

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

#256 - st.spatial.trajectory.pseudotimespace_global()

Issue - State: closed - Opened by yandouwahhh about 1 year ago - 2 comments

#255 - Dimension of 'distance' in LR permutation test

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

#254 - st.spatial.trajectory.pseudotimespace_global()

Issue - State: closed - Opened by onionsci about 1 year ago - 9 comments

#252 - st.pl.cluster_plot

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

#251 - stLearn Usage

Issue - State: closed - Opened by rialc13 about 1 year ago - 14 comments

#250 - diameter size in xenium tutorial

Issue - State: closed - Opened by revolvefire about 1 year ago - 4 comments

#249 - Installation issue on Macbook M1

Issue - State: closed - Opened by Kennyluo4 about 1 year ago - 2 comments

#248 - Some questions about CCI's Visualisations

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

#247 - about "st.pl.trajectory.tree_plot" problem

Issue - State: closed - Opened by chang202308 over 1 year ago - 7 comments

#246 - st.spatial.trajectory.pseudotime convergence error

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

#245 - "available_paths" not available

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

#244 - preprocessing steps

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

#243 - st.pl.trajectory.tree_plot issue

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

#242 - About Trajectory Analysis

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

#241 - AttributeError: 'NoneType' object has no attribute **'_get_renderer'

Issue - State: closed - Opened by Ding7928 over 1 year ago - 2 comments

#240 - AttributeError when adding annotation to clusters in trajectory analysis

Issue - State: closed - Opened by fuerzhou over 1 year ago - 4 comments

#239 - installation error

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

#238 - resize returns a copy

Issue - State: closed - Opened by schae211 over 1 year ago - 1 comment

#237 - Diagnostic plot - data does not have "nonzero-median"

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

#236 - Issue with Harmonypy

Issue - State: closed - Opened by RubyLiu-2 over 1 year ago - 3 comments

#234 - Problem with plotting "Seurat Cluster" in "stlearn" object

Issue - State: closed - Opened by suvranath1 over 1 year ago - 5 comments

#233 - Does stlearn support customly defined celltype in trajectory analysis?

Issue - State: closed - Opened by QuinceyLv over 1 year ago - 6 comments

#232 - Problem with creating "stlearn object"

Issue - State: closed - Opened by suvranath1 over 1 year ago - 4 comments

#231 - Bump flask from 2.0.3 to 2.3.2 in /stlearn/app

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

#230 - same cell type in cci

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

#229 - changing default color of cells - st.pl.cluster_scatter

Issue - State: closed - Opened by vkjain006 over 1 year ago - 3 comments

#227 - Can stLearn analyze the SpaceRanger2 data based on CytAssist-Visium FFPE ?

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

#226 - error in st.spatial.trajectory.pseudotime

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

#225 - TypingError: Failed in nopython mode pipeline (step: nopython frontend)

Issue - State: closed - Opened by jmzhang1911 over 1 year ago - 14 comments

#223 - TypeError: metaclass conflict

Issue - State: closed - Opened by tyaoi almost 2 years ago - 4 comments

#222 - cell type specific LR pairs---questions

Issue - State: closed - Opened by jinyuanchun almost 2 years ago

#221 - papers cited stlearn method

Issue - State: closed - Opened by LipingChen0607 almost 2 years ago - 2 comments

#220 - Fail to read Space Ranger output file with stlearn.Read10X.

Issue - State: closed - Opened by jingwyang almost 2 years ago - 2 comments

#219 - Error: "array_row" not found during SME

Issue - State: closed - Opened by bmlett almost 2 years ago - 9 comments

#218 - How to show figure in python console

Issue - State: closed - Opened by Feng-Zhang almost 2 years ago - 2 comments

#217 - st.pl.ccinet_plot index error

Issue - State: closed - Opened by lhock17 almost 2 years ago - 6 comments

#216 - st.pl.trajectory.tree_plot not show cropped image for each node

Issue - State: closed - Opened by xiaojjia about 2 years ago - 2 comments

#215 - Cci dev

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