Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / atarashansky/SAMap issues and pull requests
#152 - problem in intetpreting the SAMap integration results
Issue -
State: open - Opened by GGboy-Zzz 19 days ago
- 2 comments
#151 - How SAMap deal with species-specific cell types/clusters in integration?
Issue -
State: open - Opened by DiracZhu1998 3 months ago
#150 - 'coo_matrix' object has no attribute 'A'
Issue -
State: open - Opened by dnjst 3 months ago
#149 - dendrogram calculation issue
Issue -
State: open - Opened by DiracZhu1998 3 months ago
#148 - ImportError: cannot import name 'get_cmap' from 'matplotlib.cm'
Issue -
State: open - Opened by kelsell15 5 months ago
- 3 comments
#147 - Update setup.py
Pull Request -
State: closed - Opened by atarashansky 6 months ago
#146 - How to process the raw h5ad?
Issue -
State: open - Opened by JordanCTLin 6 months ago
#145 - Bug to run the SAMap algorithm
Issue -
State: open - Opened by xiangyuma1995 6 months ago
- 9 comments
#144 - Export SAMap pairs results to Seurat
Issue -
State: open - Opened by silvainp 6 months ago
#143 - Best course of action when one has multiple datasets per species
Issue -
State: closed - Opened by matejasoretic 7 months ago
- 1 comment
#142 - SAMap consistently generating a bifurcated UMAP
Issue -
State: closed - Opened by dariotommasini 8 months ago
- 7 comments
#141 - Clustering in stitched space
Issue -
State: closed - Opened by dariotommasini 9 months ago
- 22 comments
#140 - fix: incorrect _smart_expand parameter
Pull Request -
State: closed - Opened by atarashansky 9 months ago
#139 - Gene filtering parameter
Issue -
State: closed - Opened by dariotommasini 9 months ago
- 3 comments
#138 - Could alternative methods for BLAST be used?
Issue -
State: closed - Opened by Budjavac 9 months ago
- 2 comments
#137 - conda install: can't import samap
Issue -
State: open - Opened by jowodo 10 months ago
- 1 comment
#136 - Tagging Version
Issue -
State: open - Opened by jowodo 10 months ago
#135 - Reproducibility and seeding
Issue -
State: open - Opened by dariotommasini 10 months ago
- 1 comment
#134 - Combined umap for 1 cell lineage, retrieving latent representation
Issue -
State: open - Opened by nhgopee 11 months ago
#133 - sankey and chord plot error
Issue -
State: open - Opened by dsb66 11 months ago
- 12 comments
#132 - installing issues
Issue -
State: open - Opened by stevenjblair 11 months ago
#131 - Harmony integration (was closed issue #83)
Issue -
State: closed - Opened by dsb66 11 months ago
- 6 comments
#130 - how sankey_plot show more than four species
Issue -
State: open - Opened by xmChen090 11 months ago
- 7 comments
#129 - Update analysis.py
Pull Request -
State: closed - Opened by zEpoch 11 months ago
#128 - sankey_plot error
Issue -
State: open - Opened by zEpoch 11 months ago
- 5 comments
#127 - error in runing map_genes.sh
Issue -
State: open - Opened by rdf1993 12 months ago
- 1 comment
#126 - Question about neigh_from_keys parameter
Issue -
State: open - Opened by Bassi-git almost 1 year ago
- 1 comment
#125 - "ValueError: could not convert string to float" in convert_eggnog_to_homologs()
Issue -
State: open - Opened by Zaffe24 about 1 year ago
- 1 comment
#124 - AttributeError after creating SAMAP object
Issue -
State: closed - Opened by colinshew about 1 year ago
- 2 comments
#123 - Mapping scores on edges
Issue -
State: open - Opened by DinithiRajapaksha about 1 year ago
#122 - Cross-species UMAP scatter plots
Issue -
State: closed - Opened by zhongzheng1999 about 1 year ago
- 1 comment
#121 - get_mapping_scores() for cell types within same species non-zero
Issue -
State: open - Opened by dnjst about 1 year ago
- 1 comment
#120 - ModuleNotFoundError: No module named 'samalg'
Issue -
State: closed - Opened by DinithiRajapaksha about 1 year ago
- 2 comments
#119 - Multi-species cell type network plot
Issue -
State: open - Opened by dnjst about 1 year ago
- 1 comment
#118 - Gene Pair Finder Giving "ValueError: negative dimensions are not allowed"
Issue -
State: open - Opened by acgarretson about 1 year ago
- 2 comments
#117 - UMAP looks like a line when neighborhood size was determined by using cell type labels
Issue -
State: open - Opened by Evenlyeven over 1 year ago
- 5 comments
#116 - The gene expression levels after SAMap-integrated are all greater than 0
Issue -
State: closed - Opened by HYJ-hh over 1 year ago
- 2 comments
#115 - SAMap and Docker
Issue -
State: closed - Opened by avianalter over 1 year ago
- 2 comments
#114 - "ValueError: zero-size array to reduction operation" and other comments
Issue -
State: closed - Opened by avianalter over 1 year ago
#113 - How to use appropriate single cell data files as input files for SAMap correctly?
Issue -
State: closed - Opened by HYJ-hh over 1 year ago
- 1 comment
#112 - SAMAP object instantiation fails with AttributeError
Issue -
State: open - Opened by carlosj-rr over 1 year ago
- 1 comment
#111 - Installation instructions in the README are wrong
Issue -
State: closed - Opened by pnewstein over 1 year ago
- 1 comment
#110 - AttributeError: type object 'object' has no attribute 'dtype'
Issue -
State: closed - Opened by yangqi1999 over 1 year ago
- 5 comments
#109 - Clarifying expression overlap plots
Issue -
State: closed - Opened by dkeitley over 1 year ago
- 2 comments
#108 - Numba Dispatcher Issue with sm.run()
Issue -
State: open - Opened by mikepassal over 1 year ago
- 14 comments
#107 - the dtype of array is not correct
Issue -
State: open - Opened by wubaosheng over 1 year ago
#106 - Neighbourhood graph or embedding?
Issue -
State: closed - Opened by YY-SONG0718 over 1 year ago
- 2 comments
#105 - Running map_genes.sh
Issue -
State: closed - Opened by wershofe over 1 year ago
- 2 comments
#104 - transfer_annotations - removed
Issue -
State: closed - Opened by kullrich over 1 year ago
- 8 comments
#103 - Converting files
Issue -
State: closed - Opened by otoky over 1 year ago
- 2 comments
#102 - "IndexError: boolean index did not match indexed array along dimension 0" in SAMAP call
Issue -
State: closed - Opened by lb15 over 1 year ago
- 6 comments
#101 - Do noe know which reference should be choosen for doing blast
Issue -
State: closed - Opened by houruiyan almost 2 years ago
- 7 comments
#100 - sankey_plot(MappingTable, align_thr=0.05, species_order = ['pl','sc','hy'])
Issue -
State: closed - Opened by JoshuaNguyen123 almost 2 years ago
- 16 comments
#99 - "Too many values to unpack" ENRICHMENT_SCORES,NUM_ENRICHED_GENES,ENRICHED_GENES = FE.calculate_enrichment(verbose=True)
Issue -
State: closed - Opened by JoshuaNguyen123 almost 2 years ago
- 2 comments
#98 - Problem with Gp,G1,G2 = gpf.find_genes(n1,n2)
Issue -
State: closed - Opened by JoshuaNguyen123 almost 2 years ago
- 1 comment
#97 - 0 `mo` gene symbols match between the datasets and the BLAST graph.
Issue -
State: closed - Opened by houruiyan almost 2 years ago
- 4 comments
#96 - empty
Pull Request -
State: closed - Opened by atarashansky almost 2 years ago
#95 - Error in running sm.run()
Issue -
State: closed - Opened by FraMont1 almost 2 years ago
- 2 comments
#94 - FileExistsError: BLAST mapping tables with the input IDs (mo and ra) not found in the specified path.
Issue -
State: closed - Opened by houruiyan almost 2 years ago
- 3 comments
#93 - BaseException: Could not construct partition: vector::_M_default_append
Issue -
State: closed - Opened by houruiyan almost 2 years ago
- 2 comments
#92 - Error in running map_genes.sh
Issue -
State: closed - Opened by djlmt almost 2 years ago
- 2 comments
#91 - Installation issue in numpy import
Issue -
State: closed - Opened by Hrovatin almost 2 years ago
- 2 comments
#90 - Is SAMap suitable for plant scRNA-seq?
Issue -
State: closed - Opened by SCQUchenyang almost 2 years ago
- 6 comments
#89 - input formats?
Issue -
State: closed - Opened by gulfshores about 2 years ago
- 3 comments
#88 - samalg can't import.
Issue -
State: closed - Opened by Ray569743422 about 2 years ago
- 3 comments
#87 - How to calculate the cell-type specific substitution score?
Issue -
State: closed - Opened by huawen-poppy about 2 years ago
- 1 comment
#86 - Feature Request: p-values for the gene:gene pairs in genepairfinder:find_all()
Issue -
State: closed - Opened by philoel about 2 years ago
- 3 comments
#85 - An error when use sm.run(pairwise=True)
Issue -
State: closed - Opened by Smilenone about 2 years ago
- 2 comments
#84 - Functional Enrichment with GO terms not easily working
Issue -
State: closed - Opened by philoel about 2 years ago
- 13 comments
#83 - Datatset with biological replicates
Issue -
State: closed - Opened by joeyhuang401055 about 2 years ago
- 4 comments
#82 - Looking to use SAMap to analyze datasets from mouse and zebrafish single cell.
Issue -
State: closed - Opened by otoky about 2 years ago
- 4 comments
#81 - Where can I download fasta data of transcriptome/proteome for different species?
Issue -
State: closed - Opened by Smilenone about 2 years ago
- 8 comments
#80 - arrays used as indices must be of integer (or boolean) type
Issue -
State: closed - Opened by silastittes about 2 years ago
- 1 comment
#79 - Adding options for thread numbers
Pull Request -
State: closed - Opened by mys721tx over 2 years ago
#78 - "KeyError: 'dict'" with reproducible example
Issue -
State: closed - Opened by silastittes over 2 years ago
- 5 comments
#77 - key bug in transfer annotation function
Pull Request -
State: closed - Opened by chewc over 2 years ago
#76 - save_samap TypeError: can't pickle weakref objects
Issue -
State: closed - Opened by jmmusser over 2 years ago
- 1 comment
#75 - "Too many values to unpack" in sm.run()
Issue -
State: closed - Opened by philoel over 2 years ago
- 15 comments
#74 - Compute the EggNOG table
Issue -
State: closed - Opened by YY-SONG0718 over 2 years ago
- 2 comments
#73 - Error when "transfer_annotations"
Issue -
State: closed - Opened by rodrisenovilla over 2 years ago
- 2 comments
#72 - KeyError: 'tissue' in sm.samap.adata
Issue -
State: closed - Opened by wubaosheng over 2 years ago
#71 - after the 'sm.run(pairwise=True)', how to save the results of sm to our disk?
Issue -
State: closed - Opened by wubaosheng over 2 years ago
- 2 comments
#70 - ValueError: inconsistent shapes for sm.run(pairwise=True)
Issue -
State: closed - Opened by wubaosheng over 2 years ago
- 1 comment
#69 - Error when using a custom data set
Issue -
State: closed - Opened by PeiwenJi over 2 years ago
- 4 comments
#68 - Extracting knn averaged, standardized expression values from samap object
Issue -
State: closed - Opened by ivanferrreira over 2 years ago
- 1 comment
#67 - `SAMAP()` taking too long to run?
Issue -
State: closed - Opened by archavan over 2 years ago
- 9 comments
#66 - `KeyError: 'connectivities'` when running `SAMAP()`
Issue -
State: closed - Opened by archavan over 2 years ago
- 6 comments
#65 - Mapping eggnogs - code snippet
Issue -
State: closed - Opened by ivanferrreira over 2 years ago
- 1 comment
#64 - Usage of map_genes.sh
Issue -
State: closed - Opened by PeiwenJi over 2 years ago
- 2 comments
#63 - Jupyter Notebook launched from docker container crashes when importing SAMap
Issue -
State: closed - Opened by JesseDGibson over 2 years ago
- 3 comments
#62 - h5ad file
Issue -
State: closed - Opened by RhettRautsaw over 2 years ago
#61 - Seurat Integrated dataset import SAMAP
Issue -
State: closed - Opened by billadelonge almost 3 years ago
- 2 comments
#60 - export plots
Issue -
State: closed - Opened by Bassi-git almost 3 years ago
- 2 comments
#59 - get 0 gene symbols match between the datasets and the BLAST graph
Issue -
State: closed - Opened by huawen-poppy almost 3 years ago
- 23 comments
#58 - Issue running recent SAMap_vignette
Issue -
State: closed - Opened by itliao almost 3 years ago
- 1 comment
#57 - Building wheel for numba
Issue -
State: closed - Opened by billadelonge almost 3 years ago
- 14 comments
#56 - Understanding the block diagonal gene expression matrix
Issue -
State: closed - Opened by jasminelmah almost 3 years ago
- 3 comments
#55 - Calculate Mapping Scores with leiden_clusters
Issue -
State: closed - Opened by kmmika almost 3 years ago
- 3 comments
#54 - Updating transcript ids using names1 and names2
Issue -
State: closed - Opened by kmmika about 3 years ago
- 7 comments
#53 - SAMAP() function for Windows using h5ad files does not work
Issue -
State: closed - Opened by JavBurgoa about 3 years ago
- 3 comments