BiomedicalMachineLearning/stLearn issues and pull requests

#214 - Problem with st.tl.cci.run_cci()

Issue - State: closed - Opened by xfchen0912 about 2 years ago - 7 comments

#213 - Cci dev

Pull Request - State: closed - Opened by duypham2108 about 2 years ago

#212 - fix: fix sphinx gallery

Pull Request - State: closed - Opened by duypham2108 about 2 years ago

#211 - Psts fix

Pull Request - State: closed - Opened by duypham2108 about 2 years ago

#210 - fix: fix loc error

Pull Request - State: closed - Opened by duypham2108 about 2 years ago

#209 - problem about lr subunit

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

#208 - fix: remove Panel import

Pull Request - State: closed - Opened by duypham2108 about 2 years ago

#207 - fix: fix zoom trajectories

Pull Request - State: closed - Opened by duypham2108 about 2 years ago

#206 - Where is the input data in CCI manual?

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

#205 - feature: add zoom feature for plot

Pull Request - State: closed - Opened by duypham2108 about 2 years ago

#204 - Psts fix

Pull Request - State: closed - Opened by duypham2108 about 2 years ago

#203 - PSTS with Xenium data

Issue - State: closed - Opened by duypham2108 about 2 years ago - 8 comments
Labels: enhancement

#202 - fix: fix the speed performance of psts, change the tree_plot

Pull Request - State: closed - Opened by duypham2108 about 2 years ago

#201 - Fix warnings

Pull Request - State: closed - Opened by duypham2108 about 2 years ago

#200 - some questions about transition markers detection

Issue - State: closed - Opened by ShawnXzz about 2 years ago - 5 comments

#199 - Same genes in LR interaction

Issue - State: closed - Opened by ZheFrench about 2 years ago - 13 comments

#198 - runtime about cci

Issue - State: closed - Opened by jinyuanchun about 2 years ago - 5 comments

#197 - FileNotFoundError

Issue - State: closed - Opened by xiao-kong-long about 2 years ago - 2 comments

#196 - stlearn.pl.deconvolution_plot's results without legend

Issue - State: closed - Opened by ZgtL15 about 2 years ago - 2 comments

#195 - Visualizing cci results with Stereo_seq

Issue - State: closed - Opened by Madong1110 about 2 years ago - 2 comments

#194 - cell type specific LR pairs like #182

Issue - State: closed - Opened by jinyuanchun about 2 years ago - 8 comments

#193 - st.pl.cci_check issue

Issue - State: closed - Opened by jk86754 about 2 years ago - 1 comment

#192 - Problem with GO enrichment analysis

Issue - State: closed - Opened by jk86754 about 2 years ago - 3 comments

#191 - Subset stlearn object based on cell barcodes

Issue - State: closed - Opened by jk86754 about 2 years ago - 2 comments

#190 - fix_decon_plot_legend

Pull Request - State: closed - Opened by xiao233333 about 2 years ago

#189 - data read in error

Issue - State: closed - Opened by jk86754 about 2 years ago - 14 comments

#188 - question about CCI

Issue - State: closed - Opened by jinyuanchun about 2 years ago - 5 comments

#187 - About stSME clustering

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

#186 - how can i understand stlearn.create_stlearn() Parameters : scale

Issue - State: closed - Opened by jinyuanchun about 2 years ago - 4 comments

#185 - Qustion about P-value adjustment in Cell-Cell Interaction Analysis

Issue - State: closed - Opened by LipingChen0607 over 2 years ago - 9 comments

#184 - label_transfer_bc.csv

Issue - State: closed - Opened by jinyuanchun over 2 years ago - 1 comment

#183 - Error in SME clustering

Issue - State: closed - Opened by urowufei over 2 years ago - 2 comments

#182 - cell type specific LR pairs

Issue - State: closed - Opened by skim245 over 2 years ago - 1 comment

#181 - Some questions about trajectory analysis

Issue - State: closed - Opened by ShawnXzz over 2 years ago - 3 comments

#180 - add: concatenate spatial feature

Pull Request - State: closed - Opened by duypham2108 over 2 years ago

#179 - add: concatenate spatial feature

Pull Request - State: closed - Opened by duypham2108 over 2 years ago

#178 - Find CCI on simulated data - hyperparameters and runtime

Issue - State: closed - Opened by joeyhbao over 2 years ago - 1 comment

#177 - Dev psts

Pull Request - State: closed - Opened by duypham2108 over 2 years ago

#176 - manually combine the images for different array dimensions

Issue - State: closed - Opened by LipingChen0607 over 2 years ago - 7 comments

#175 - problem in GO enrichment analysis of LR

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

#174 - Spatial deconvolution visualization problem

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

#173 - Unable to run trajectory pseudotime analysis on win11

Issue - State: closed - Opened by mvpsc30 over 2 years ago - 2 comments

#172 - A question about ‘st.pl.cluster_plot’

Issue - State: closed - Opened by ShawnXzz over 2 years ago - 2 comments

#171 - question regarding the root and list_clusters

Issue - State: closed - Opened by JuanXie19 over 2 years ago - 3 comments

#170 - clusters are not available to construct the spatial trajectory

Issue - State: closed - Opened by JuanXie19 over 2 years ago - 2 comments

#169 - arguments order in global level of PSTS method

Issue - State: closed - Opened by JuanXie19 over 2 years ago - 8 comments

#168 - local spatial trajectory inference

Issue - State: closed - Opened by JuanXie19 over 2 years ago - 1 comment

#167 - Pseudotime analysis for MERfish

Issue - State: closed - Opened by ShawnXzz over 2 years ago - 4 comments

#166 - fix: DBSCAN min_samples error

Pull Request - State: closed - Opened by duypham2108 over 2 years ago

#165 - unable to run spatial trajectory

Issue - State: closed - Opened by JuanXie19 over 2 years ago - 3 comments

#164 - cellchat export & figure modification

Issue - State: closed - Opened by skim245 over 2 years ago - 2 comments

#163 - AssertionError

Issue - State: closed - Opened by SadarAzmoun over 2 years ago - 1 comment

#162 - UnsupportedError

Issue - State: closed - Opened by skim245 over 2 years ago - 2 comments

#161 - Find CCI on simulated data

Issue - State: closed - Opened by joeyhbao over 2 years ago - 3 comments

#160 - Predicting significant CCIs

Issue - State: closed - Opened by sailseem over 2 years ago - 7 comments

#159 - tensorflow error

Issue - State: closed - Opened by februaryfang over 2 years ago - 5 comments

#158 - Installation and requirements of Louvain and leidenalg

Issue - State: closed - Opened by TehseusKunka over 2 years ago - 1 comment

#157 - Errors in running st.tl.cci.run

Issue - State: closed - Opened by anchormok over 2 years ago - 10 comments

#156 - How use `gene_plot` to show continuous columns in `adata.obs`

Issue - State: closed - Opened by eleozzr over 2 years ago - 2 comments

#155 - Interactive dev

Pull Request - State: closed - Opened by duypham2108 over 2 years ago

#154 - build(deps): bump tensorflow from 2.7.0 to 2.8.0

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#153 - build(deps): bump tensorflow from 2.7.0 to 2.7.1

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#152 - update: config and docs for 0.4.0

Pull Request - State: closed - Opened by duypham2108 almost 3 years ago

#151 - Error when using K-means clustering on stSME

Issue - State: closed - Opened by peicai almost 3 years ago - 2 comments

#150 - Update example and plot functions

Pull Request - State: closed - Opened by duypham2108 almost 3 years ago

#149 - New stLearn CCI analysis

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

#148 - fix: add fulres to read spatial data

Pull Request - State: closed - Opened by duypham2108 almost 3 years ago

#147 - build(deps): bump pillow from 8.3.2 to 9.0.0

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#146 - DLL load failed while importing utilsextension

Issue - State: closed - Opened by bioinflix almost 3 years ago - 5 comments

#145 - fix: convert RGBA to RGB

Pull Request - State: closed - Opened by duypham2108 almost 3 years ago

#144 - update: update packages version

Pull Request - State: closed - Opened by duypham2108 almost 3 years ago

#143 - Something wrong in plot

Issue - State: closed - Opened by anchormok almost 3 years ago - 6 comments

#142 - Error from 2nd step in cell-cell interaction

Issue - State: closed - Opened by DecodeGenome almost 3 years ago - 2 comments

#141 - Problem when reproducing Cell-to-cell Interaction Part

Issue - State: closed - Opened by YistYU almost 3 years ago - 1 comment

#140 - fix: convert RGBA to RGB

Pull Request - State: closed - Opened by xiao233333 almost 3 years ago
Labels: enhancement

#139 - Adding high resolution image

Issue - State: closed - Opened by tpentim almost 3 years ago - 1 comment

#138 - st.pl.deconvolution_plot() size error

Issue - State: closed - Opened by lsudupe about 3 years ago - 1 comment

#137 - Error when using contour

Issue - State: closed - Opened by ccruizm about 3 years ago - 1 comment

#136 - build(deps): bump tensorflow from 2.6.0 to 2.6.1

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#135 - transferring seurat labels to stLearn

Issue - State: closed - Opened by iphon5 about 3 years ago - 8 comments

#133 - stLearn Cell-cell interaction analysis

Issue - State: closed - Opened by evenDDDDD about 3 years ago - 3 comments

#132 - problem about finding file "label_transfer_bc.csv"

Issue - State: closed - Opened by zhengdongfeng about 3 years ago - 10 comments

#113 - Function of interactive not works

Issue - State: closed - Opened by jipeifeng over 3 years ago - 4 comments
Labels: bug

#86 - Setting root for Pseudotime analysis

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

GitHub / BiomedicalMachineLearning/stLearn issues and pull requests