Ecosyste.ms: Issues

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

GitHub / lilab-bcb/pegasus issues and pull requests

#313 - Potential Bug in Infer Doublets

Issue - State: open - Opened by hl-xue 4 months ago

#311 - How to Embed BBKNN Results into MultimodalData?

Issue - State: open - Opened by x1han 4 months ago

#310 - Questions about installation of the version "infercnv"

Issue - State: open - Opened by Richard-D-Watson 4 months ago - 1 comment

#309 - Bug fix for deseq2 function with one contrast

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

#308 - Fix mouse lung markers not found issue

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

#307 - Added bimodality index to doublet detection

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

#306 - Fix bug in writing GSEA results to file

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

#305 - Reorganize GSEA function

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

#304 - Deseq2 allows inference with multiple contrasts in the same model

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

#303 - Fix deseq2

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

#302 - Several updates

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

#301 - Reorganize GSEA functions

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

#300 - Reorganize pseudobulk and deseq2 functions

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

#299 - using cellbender outputs

Issue - State: closed - Opened by jackhump 6 months ago - 2 comments

#298 - Added function to find NMF programs (searching K)

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

#297 - Reorganize pseudobulk analysis functions

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

#296 - Enforce dissimilarity matrix with main diagonal 0s

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

#295 - New version of dendrogram

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

#294 - Improve Scatter and Spatial plots

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

#293 - Allow change label font size in GSEA plot

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

#292 - Add show_only_expressed option to dotplot

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

#291 - Spatial and Scatter plot

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

#290 - Enforce dense or csr_matrix type for calculate_z_score function

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

#289 - Boli

Pull Request - State: closed - Opened by bli25 9 months ago

#288 - Inconsistent z-score calculation for CSC and CSR sparse matrices

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

#287 - Harmony data integration accepts multiple attributes as batch key

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

#286 - Fix heatmap

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

#285 - Update CI test

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

#284 - Plot skip attributes/genes not in data

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

#283 - Fix violin plot for Seaborn v0.13+

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

#282 - Updated heatmap function

Pull Request - State: closed - Opened by bli25 11 months ago

#281 - Address a few frequent matrix dtype conversion errors

Pull Request - State: closed - Opened by hvbakel 11 months ago - 4 comments

#279 - Expose online_batch_size in nmf and integrative_nmf functions

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

#278 - Fix a typo in human_lung cell marker JSON file

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

#277 - Improve plotting functions

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

#276 - only convert sparse matrices to numpy arrays

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

#275 - Improve doublet detection and cell markers

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

#274 - Fixed a typo

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

#273 - Subset using a list of barcodes

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

#271 - Error with pegasus.calc_kBET

Issue - State: open - Opened by hl-xue over 1 year ago

#270 - Added CD4 CTL markers

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

#269 - Updated T cell subtype markers

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

#268 - Update doublet_detection.py

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

#267 - Updated NK cell and NK subtype markers

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

#266 - how to subplot in pegasus?

Issue - State: closed - Opened by x1han over 1 year ago - 2 comments

#265 - Error with FLE

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

#264 - Updated neutrophil markers

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

#263 - Updated neutrophil markers

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

#262 - Fix bug for `split_one_cluster`

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

#261 - Make code compatible with Pandas 2.0

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

#260 - Updated human lung and immune markers

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

#259 - counts.log_norm+scale in pegasus vs. scale.data in Seurat and scanpy

Issue - State: closed - Opened by x1han over 1 year ago - 3 comments

#258 - Fix divide by zero issue in integrative_nmf

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

#257 - scTransform support

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

#256 - 【Bug】leiden or louvain clustering error

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

#255 - Added Germinal Center B cell markers

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

#254 - on disk reading of a large h5ad file

Issue - State: open - Opened by hoondy about 2 years ago

#253 - 1.2.0 L/S method

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

#252 - Replaced python-igraph with igraph and requires igraph <= 0.9.10 to m…

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

#251 - Added normalize, log1p, renamed arcsinh_transform to arcsinh, and ena…

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

#250 - Several important updates

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

#249 - Update test_hashing_citeseq.py

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

#248 - Mismatch dtype for diff_expr.py

Issue - State: open - Opened by tsigalko2003 over 2 years ago

#247 - How can I plot diffusion map by DC2 and DC3?

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

#246 - Prepare for v1.6.0 release

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

#245 - scvi-tools

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

#244 - SCVITOOLS updates

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

#243 - pegasus.fgsea NOT work with MOUSE genome

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

#242 - For v1.5.0 release

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

#241 - L/S method is deprecated in version 1.4.5?

Issue - State: closed - Opened by niehu2018 over 2 years ago - 3 comments

#240 - Tutorial

Pull Request - State: closed - Opened by rocherroche almost 3 years ago - 6 comments

#239 - Fgsea

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

#238 - Deseq2

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

#237 - Implement pseudo-bulk generation function

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

#236 - error when using aggregate_matrices to aggregate two multimodaldata

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

#235 - Expose `legend_fontsize` in `scatter` function to users

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

#234 - Enforce recalculating kNN for subclustering

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

#233 - Update nearest_neighbors.py

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

#232 - Update docs

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

#231 - poetry files

Pull Request - State: closed - Opened by rocherroche almost 3 years ago - 1 comment

#230 - pegasus multi install

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

#229 - Adapt to umap v0.5.2 & remove gprofiler

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

#228 - Add spatial plot function for 10X Visium data

Pull Request - State: closed - Opened by yihming almost 3 years ago - 1 comment

#227 - Cell cycle regress before run_scanorama?

Issue - State: open - Opened by Zifeng-L almost 3 years ago

#226 - Error reporting when run "pg.fle(data, rep=harmony_key)"

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

#225 - Do not need batch attr be Channel and eliminate Channels

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

#224 - test

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

#223 - Updated preprocessing for spatial analysis

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

#222 - Is there any academic paper for pegasus?

Issue - State: closed - Opened by tangmaomao16 almost 3 years ago - 1 comment

#221 - Update batch_correction.py

Pull Request - State: closed - Opened by hoondy about 3 years ago - 1 comment

#220 - clustering based on a subset of cells

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

#219 - update hashing & cite-seq test scripts

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

#218 - Add calculate_z_score function

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

#217 - Updated signature score

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

#216 - Update requirements.txt

Pull Request - State: closed - Opened by hoondy about 3 years ago - 1 comment

#215 - Allow run_harmony use GPU

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

#214 - Updated nmf and pipeline for generating h5ad files

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