Ecosyste.ms: Issues

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

GitHub / theislab/single-cell-tutorial issues and pull requests

#101 - How can we change the plot shape (not only using dot) of UMAP in Scanpy?

Issue - State: closed - Opened by melancholy12 over 2 years ago - 2 comments

#99 - sc.tl.rank_genes_groups and pct1 & pct2 output

Issue - State: closed - Opened by TRakesh0121 over 2 years ago - 1 comment

#98 - Can we also use Seurat v3 v4 or liger in scanpy or python?

Issue - State: closed - Opened by melancholy12 over 2 years ago - 7 comments

#97 - Key Error "base" in section "marker genes & annotation"

Issue - State: closed - Opened by Mari123i over 2 years ago - 4 comments

#96 - Batch correction with combat causes Jupyter kernel to die

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

#95 - R command throw UnicodeDecodeError

Issue - State: open - Opened by Mari123i over 2 years ago - 3 comments

#94 - Too few Duodenum cells

Issue - State: closed - Opened by Mari123i over 2 years ago - 1 comment

#93 - Error

Issue - State: closed - Opened by skr3178 over 2 years ago - 1 comment

#91 - Damaged tar archive

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

#90 - Normalizing subsetted data

Issue - State: open - Opened by oligomyeggo over 2 years ago - 1 comment

#89 - Interpretation of rank_genes_groups

Issue - State: closed - Opened by Lavieenrose123 over 2 years ago - 1 comment

#88 - Reference for downloading the dataset

Issue - State: open - Opened by Sangram-Rout over 2 years ago - 1 comment

#87 - combine clusters after clustering

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

#86 - clustering resolutions--how to tune

Issue - State: closed - Opened by DUAN-GAO almost 3 years ago - 3 comments

#84 - searborn.distplot() is deprecated

Issue - State: open - Opened by le-ander almost 3 years ago - 1 comment

#83 - Running in pure python env: in a .py file

Issue - State: open - Opened by DUAN-GAO almost 3 years ago - 1 comment

#82 - ValueError: cannot reindex from a duplicate axis

Issue - State: closed - Opened by DUAN-GAO almost 3 years ago - 7 comments

#81 - RRuntimeError: Error in validObject(.Object) :

Issue - State: open - Opened by vincentxu199112 almost 3 years ago - 1 comment

#79 - Batch correction runtime warning: Divide by zero

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

#78 - Choice of gene sets for cell cycle scoring

Issue - State: open - Opened by fbnrst almost 3 years ago - 1 comment

#77 - Add fixes for 2021 container

Pull Request - State: open - Opened by Zethson about 3 years ago - 4 comments

#76 - TypeError when trying to add known marker genes

Issue - State: closed - Opened by oligomyeggo about 3 years ago - 7 comments

#75 - louvain vs leiden

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

#74 - Package versions in .yml file

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

#73 - What type of matrix should `score_genes` be applied to?

Issue - State: open - Opened by liuzj039 about 3 years ago

#72 - Resetting Max Buffer Size for Jupyter Notebook

Issue - State: closed - Opened by JakeLehle about 3 years ago - 5 comments

#71 - Error in dataloader

Issue - State: closed - Opened by wiedemer about 3 years ago - 7 comments

#70 - Is it necessary to specify `n_genes` in box 35

Issue - State: closed - Opened by yugeji over 3 years ago - 1 comment

#69 - Update sc_tutorial_environment.yml

Pull Request - State: closed - Opened by herokoking over 3 years ago - 1 comment

#68 - Cannot open jupyter lab in docker container

Issue - State: closed - Opened by dong7422 over 3 years ago - 1 comment

#67 - (Report a problem) Cannot reindex from a duplicate axis

Issue - State: closed - Opened by Teerapon789 over 3 years ago - 8 comments

#65 - Subclustering

Issue - State: closed - Opened by lu77777777 over 3 years ago - 4 comments

#64 - visualization for UMAP error

Issue - State: closed - Opened by lu77777777 over 3 years ago

#62 - R language in .py file

Issue - State: closed - Opened by lu77777777 over 3 years ago - 1 comment

#61 - AttributeError: module 'louvain' has no attribute 'set_rng_seed'

Issue - State: closed - Opened by lu77777777 over 3 years ago - 1 comment

#60 - %%R -i data_mat -i input_groups -o size_factors

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

#59 - can't set up environment

Issue - State: closed - Opened by JuanTan628 over 3 years ago - 9 comments

#58 - Notebook update to January 2021 version

Pull Request - State: open - Opened by LuckyMD over 3 years ago - 3 comments

#57 - ValueError: cannot reindex from a duplicate axis

Issue - State: closed - Opened by Leran10 over 3 years ago - 10 comments

#56 - no latest tag for Docker container

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

#55 - normalization: scran vs neg. binomial regression (sctransform)

Issue - State: closed - Opened by grst almost 4 years ago - 7 comments

#54 - Add missing files for docker container building

Pull Request - State: open - Opened by le-ander almost 4 years ago - 17 comments

#53 - Make concat function call compatible with updated scanpy

Pull Request - State: closed - Opened by lzhus almost 4 years ago - 3 comments

#52 - sc.pp.neighbors(adata_pp)

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

#51 - Building container image failes due to missing files

Issue - State: closed - Opened by serverhorror almost 4 years ago - 8 comments

#50 - InvalidIndexError: Reindexing only valid with uniquely valued Index objects

Issue - State: closed - Opened by 814471489 almost 4 years ago - 4 comments

#49 - %%R -i data_ent

Issue - State: open - Opened by hatuyen4994 almost 4 years ago - 21 comments

#48 - adata.concatenate

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

#47 - Update dockerfile

Pull Request - State: closed - Opened by le-ander almost 4 years ago - 1 comment

#46 - Add Dockerfile for sc-analysis Container

Pull Request - State: closed - Opened by le-ander almost 4 years ago

#45 - Dockerfile is not visible

Issue - State: closed - Opened by serverhorror almost 4 years ago - 8 comments

#43 - Problems when installing package"Slingshot"and "Monocle"

Issue - State: closed - Opened by satellite119 about 4 years ago - 8 comments

#42 - Kernel restarting when concatenating

Issue - State: closed - Opened by omanor about 4 years ago - 3 comments

#41 - Problem with adata concatenation

Issue - State: closed - Opened by davidtourigny over 4 years ago - 12 comments

#40 - computeSumFactors(data_mat, clusters=input_groups, min.mean=0.1) gives error

Issue - State: closed - Opened by ariberar over 4 years ago - 16 comments

#39 - mt fraction calculation

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

#36 - Different outputs

Issue - State: closed - Opened by evenDDDDD over 4 years ago - 3 comments

#35 - Best practices for using regress_out?

Issue - State: closed - Opened by oligomyeggo over 4 years ago - 11 comments

#34 - adata.var['gene_id-1']

Issue - State: closed - Opened by yuGithuuub over 4 years ago

#33 - TypeError: Callable[[arg, ...], result]: each arg must be a type. Got Ellipsis.

Issue - State: closed - Opened by jjaa-mp over 4 years ago - 1 comment

#32 - Issues with sc.pp.highly_variable_genes following tutorial

Issue - State: closed - Opened by oligomyeggo over 4 years ago - 3 comments

#31 - Error on "Making variable names unique for controlled concatenation."

Issue - State: closed - Opened by aheravi over 4 years ago - 1 comment

#30 - scanpy.plotting.palettes' has no attribute 'default_64

Issue - State: closed - Opened by f6v over 4 years ago - 1 comment

#29 - ComBat Error

Issue - State: closed - Opened by Zifeng-L over 4 years ago - 6 comments

#27 - Problem correcting batches with Combat

Issue - State: closed - Opened by ccruizm over 4 years ago - 5 comments

#26 - select highly-variable genes

Issue - State: closed - Opened by jphe over 5 years ago - 3 comments

#25 - Error in samples concatenation

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

#24 - R libraries not accessible

Issue - State: closed - Opened by mumichae about 5 years ago - 17 comments

#23 - Get environment setup info

Issue - State: closed - Opened by mbuttner about 5 years ago - 1 comment

#22 - Error in differential expression analysis

Issue - State: closed - Opened by Vyoming about 5 years ago - 1 comment

#21 - Key error with gene_id-1

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

#20 - MAST returns natural log, not log2FC

Issue - State: closed - Opened by le-ander about 5 years ago - 3 comments

#19 - Fixed folder name

Pull Request - State: closed - Opened by federicomarini about 5 years ago - 9 comments

#18 - Concatenate files error

Issue - State: closed - Opened by davidepisu about 5 years ago - 22 comments

#17 - Unable to deploy the .yml - Docker enhancement request

Issue - State: closed - Opened by marshelma about 5 years ago - 11 comments
Labels: enhancement

#16 - cleaner typo fix

Pull Request - State: closed - Opened by ttriche about 5 years ago - 1 comment

#15 - fix typo

Pull Request - State: closed - Opened by ttriche about 5 years ago - 1 comment

#14 - sc.tl.marker_gene_overlap error

Issue - State: closed - Opened by JuHey over 5 years ago - 3 comments

#13 - Issue with rgl package when trying to load slingshot

Issue - State: closed - Opened by brennerUT over 5 years ago - 7 comments

#12 - Converting between sparse and dense matrices

Issue - State: closed - Opened by PattF over 5 years ago - 3 comments

#11 - In vivo dataset comparisons

Issue - State: closed - Opened by PattF over 5 years ago - 3 comments

#10 - Error when assigning variable names and gene id columns

Issue - State: closed - Opened by PattF over 5 years ago - 1 comment

#9 - Use scanpy combat implementation

Issue - State: closed - Opened by le-ander over 5 years ago - 1 comment

#8 - Get errors when performing sc.pp.highly_variable_genes!

Issue - State: closed - Opened by jipeifeng over 5 years ago - 17 comments

#7 - Running Slingshot through rpy2 fails with pandas v0.24

Issue - State: closed - Opened by le-ander over 5 years ago - 3 comments

#6 - Aesthetics must be either length 1 or the same as the data (87): fill

Issue - State: closed - Opened by le-ander over 5 years ago - 6 comments

#5 - Could not find function clusterExperiment()

Issue - State: closed - Opened by le-ander over 5 years ago - 3 comments

#4 - Jupyter notebook kernel crashes silently: Intel OMP

Issue - State: closed - Opened by le-ander over 5 years ago - 5 comments

#2 - ComBat error "TypeError: data type not understood"

Issue - State: closed - Opened by LuckyMD over 5 years ago - 14 comments

#1 - rpy2 does not support sparse matrices

Issue - State: closed - Opened by LuckyMD over 5 years ago - 3 comments