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
#102 - executing sc.tl.rank_genes_groups() function on tutorial data provides incorrect results
Issue -
State: closed - Opened by Monkeyninjaw over 2 years ago
- 1 comment
#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
#100 - get the clustering and subclustering results differ from those given in example
Issue -
State: closed - Opened by imemorizedpi over 2 years ago
#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
#92 - FileNotFoundError: [Errno 2] No such file or directory: '../Macosko_cell_cycle_genes.txt'
Issue -
State: closed - Opened by skr3178 over 2 years ago
- 2 comments
#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
#85 - numpy.core._exceptions.MemoryError: Unable to allocate 926. GiB for an array with shape (6794880, 36601) and data type float32
Issue -
State: closed - Opened by DUAN-GAO almost 3 years ago
- 1 comment
#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
#80 - ValueError: 'Enterocyte mature' is not a valid category for 'louvain_r0.5_entero_sub'
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
#66 - computeSumFactors run error (Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"matrix", "character"’)
Issue -
State: closed - Opened by rdcwuyy over 3 years ago
- 7 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
#63 - %%R -i data_mat -i input_groups -o size_factors size_factors = computeSumFactors(data_mat, clusters=input_groups, min.mean=0.1)
Issue -
State: closed - Opened by lu77777777 over 3 years ago
- 3 comments
#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
#44 - concatenation issue persists after commenting out two lines as instructed in issue #41
Issue -
State: closed - Opened by SuhanG17 about 4 years ago
- 4 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
#28 - Exception: Data must be 1-dimensional when plotting new marker genes in jupyter notebook
Issue -
State: closed - Opened by federicaress over 4 years ago
- 15 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
#3 - Monocle: Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : Polygon edge not found
Issue -
State: closed - Opened by le-ander over 5 years ago
- 2 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