atarashansky/SAMap issues and pull requests

#148 - ImportError: cannot import name 'get_cmap' from 'matplotlib.cm'

Issue - State: open - Opened by kelsell15 about 2 months ago - 3 comments

#147 - Update setup.py

Pull Request - State: closed - Opened by atarashansky 2 months ago

#146 - How to process the raw h5ad?

Issue - State: open - Opened by JordanCTLin 3 months ago

#145 - Bug to run the SAMap algorithm

Issue - State: open - Opened by xiangyuma1995 3 months ago - 9 comments

#144 - Export SAMap pairs results to Seurat

Issue - State: open - Opened by silvainp 3 months ago

#143 - Best course of action when one has multiple datasets per species

Issue - State: closed - Opened by matejasoretic 4 months ago - 1 comment

#142 - SAMap consistently generating a bifurcated UMAP

Issue - State: closed - Opened by dariotommasini 5 months ago - 7 comments

#141 - Clustering in stitched space

Issue - State: closed - Opened by dariotommasini 6 months ago - 22 comments

#140 - fix: incorrect _smart_expand parameter

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

#139 - Gene filtering parameter

Issue - State: closed - Opened by dariotommasini 6 months ago - 3 comments

#138 - Could alternative methods for BLAST be used?

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

#137 - conda install: can't import samap

Issue - State: open - Opened by jowodo 7 months ago - 1 comment

#136 - Tagging Version

Issue - State: open - Opened by jowodo 7 months ago

#135 - Reproducibility and seeding

Issue - State: open - Opened by dariotommasini 7 months ago - 1 comment

#134 - Combined umap for 1 cell lineage, retrieving latent representation

Issue - State: open - Opened by nhgopee 8 months ago

#133 - sankey and chord plot error

Issue - State: open - Opened by dsb66 8 months ago - 8 comments

#132 - installing issues

Issue - State: open - Opened by stevenjblair 8 months ago

#131 - Harmony integration (was closed issue #83)

Issue - State: closed - Opened by dsb66 8 months ago - 6 comments

#130 - how sankey_plot show more than four species

Issue - State: open - Opened by xmChen090 8 months ago - 4 comments

#129 - Update analysis.py

Pull Request - State: closed - Opened by zEpoch 8 months ago

#128 - sankey_plot error

Issue - State: open - Opened by zEpoch 8 months ago - 5 comments

#127 - error in runing map_genes.sh

Issue - State: open - Opened by rdf1993 8 months ago - 1 comment

#126 - Question about neigh_from_keys parameter

Issue - State: open - Opened by Bassi-git 9 months ago - 1 comment

#125 - "ValueError: could not convert string to float" in convert_eggnog_to_homologs()

Issue - State: open - Opened by Zaffe24 9 months ago - 1 comment

#124 - AttributeError after creating SAMAP object

Issue - State: closed - Opened by colinshew 10 months ago - 2 comments

#123 - Mapping scores on edges

Issue - State: open - Opened by DinithiRajapaksha 10 months ago

#122 - Cross-species UMAP scatter plots

Issue - State: closed - Opened by zhongzheng1999 10 months ago - 1 comment

#121 - get_mapping_scores() for cell types within same species non-zero

Issue - State: open - Opened by dnjst 11 months ago - 1 comment

#120 - ModuleNotFoundError: No module named 'samalg'

Issue - State: closed - Opened by DinithiRajapaksha 12 months ago - 2 comments

#119 - Multi-species cell type network plot

Issue - State: open - Opened by dnjst 12 months ago - 1 comment

#118 - Gene Pair Finder Giving "ValueError: negative dimensions are not allowed"

Issue - State: open - Opened by acgarretson 12 months ago - 1 comment

#117 - UMAP looks like a line when neighborhood size was determined by using cell type labels

Issue - State: open - Opened by Evenlyeven about 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 about 1 year ago - 2 comments

#115 - SAMap and Docker

Issue - State: closed - Opened by avianalter about 1 year ago - 2 comments

#114 - "ValueError: zero-size array to reduction operation" and other comments

Issue - State: closed - Opened by avianalter about 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 about 1 year ago - 1 comment

#112 - SAMAP object instantiation fails with AttributeError

Issue - State: open - Opened by carlosj-rr about 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 over 1 year ago - 7 comments

#100 - sankey_plot(MappingTable, align_thr=0.05, species_order = ['pl','sc','hy'])

Issue - State: closed - Opened by JoshuaNguyen123 over 1 year 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 over 1 year ago - 2 comments

#98 - Problem with Gp,G1,G2 = gpf.find_genes(n1,n2)

Issue - State: closed - Opened by JoshuaNguyen123 over 1 year ago - 1 comment

#97 - 0 `mo` gene symbols match between the datasets and the BLAST graph.

Issue - State: closed - Opened by houruiyan over 1 year ago - 4 comments

#96 - empty

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

#95 - Error in running sm.run()

Issue - State: closed - Opened by FraMont1 over 1 year 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 over 1 year ago - 3 comments

#93 - BaseException: Could not construct partition: vector::_M_default_append

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

#92 - Error in running map_genes.sh

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

#91 - Installation issue in numpy import

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

#90 - Is SAMap suitable for plant scRNA-seq?

Issue - State: closed - Opened by SCQUchenyang over 1 year ago - 6 comments

#89 - input formats?

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

#88 - samalg can't import.

Issue - State: closed - Opened by Ray569743422 almost 2 years ago - 3 comments

#87 - How to calculate the cell-type specific substitution score?

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

#85 - An error when use sm.run(pairwise=True)

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

#84 - Functional Enrichment with GO terms not easily working

Issue - State: closed - Opened by philoel almost 2 years ago - 13 comments

#83 - Datatset with biological replicates

Issue - State: closed - Opened by joeyhuang401055 almost 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 almost 2 years ago - 4 comments

#81 - Where can I download fasta data of transcriptome/proteome for different species?

Issue - State: closed - Opened by Smilenone almost 2 years ago - 8 comments

#80 - arrays used as indices must be of integer (or boolean) type

Issue - State: closed - Opened by silastittes almost 2 years ago - 1 comment

#79 - Adding options for thread numbers

Pull Request - State: closed - Opened by mys721tx about 2 years ago

#78 - "KeyError: 'dict'" with reproducible example

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

#77 - key bug in transfer annotation function

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

#76 - save_samap TypeError: can't pickle weakref objects

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

#75 - "Too many values to unpack" in sm.run()

Issue - State: closed - Opened by philoel about 2 years ago - 15 comments

#74 - Compute the EggNOG table

Issue - State: closed - Opened by YY-SONG0718 about 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

GitHub / atarashansky/SAMap issues and pull requests