atarashansky/SAMap

Issues

• problem in intetpreting the SAMap integration results

  #152 opened a month ago by GGboy-Zzz
  0

• Gene Pair Finder Giving "ValueError: negative dimensions are not allowed"

  #118 opened a year ago by acgarretson
  2

• sankey and chord plot error

  #133 opened a year ago by dsb66
  12

• How SAMap deal with species-specific cell types/clusters in integration?

  #151 opened 4 months ago by DiracZhu1998
  0

• 'coo_matrix' object has no attribute 'A'

  #150 opened 4 months ago by dnjst
  0

• how sankey_plot show more than four species

  #130 opened a year ago by xmChen090
  7

• dendrogram calculation issue

  #149 opened 4 months ago by DiracZhu1998
  0

• ImportError: cannot import name 'get_cmap' from 'matplotlib.cm'

  #148 opened 5 months ago by kelsell15
  3

• Cross-species UMAP scatter plots

  #122 opened 6 months ago by zhongzheng1999
  1

• Numba Dispatcher Issue with sm.run()

  #108 opened 2 years ago by mikepassal
  14

• Bug to run the SAMap algorithm

  #145 opened 6 months ago by xiangyuma1995
  9

• How to process the raw h5ad?

  #146 opened 6 months ago by jordan841220
  0

• Export SAMap pairs results to Seurat

  #144 opened 6 months ago by silvainp
  0

• Reproducibility and seeding

  #135 opened a year ago by dariotommasini
  1

• Best course of action when one has multiple datasets per species

  #143 opened 7 months ago by matejasoretic
  1

• SAMap consistently generating a bifurcated UMAP

  #142 opened 8 months ago by dariotommasini
  7

• Clustering in stitched space

  #141 opened 9 months ago by dariotommasini
  22

• Gene filtering parameter

  #139 opened 9 months ago by dariotommasini
  3

• Could alternative methods for BLAST be used?

  #138 opened 10 months ago by Budjavac
  2

• "ValueError: could not convert string to float" in convert_eggnog_to_homologs()

  #125 opened a year ago by Zaffe24
  1

• conda install: can't import samap

  #137 opened 10 months ago by jowodo
  1

• Tagging Version

  #136 opened 10 months ago by jowodo
  0

• error in runing map_genes.sh

  #127 opened a year ago by rdf1993
  1

• Multi-species cell type network plot

  #119 opened a year ago by dnjst
  1

• Combined umap for 1 cell lineage, retrieving latent representation

  #134 opened a year ago by nhgopee
  0

• sankey_plot error

  #128 opened a year ago by zEpoch
  5

• Harmony integration (was closed issue #83)

  #131 opened a year ago by dsb66
  6

• installing issues

  #132 opened a year ago by stevenjblair
  0

• Question about neigh_from_keys parameter

  #126 opened a year ago by Bassi-git
  1

• AttributeError after creating SAMAP object

  #124 opened a year ago by colinshew
  2

• Mapping scores on edges

  #123 opened a year ago by DinithiRajapaksha
  0

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

  #121 opened a year ago by dnjst
  1

• ModuleNotFoundError: No module named 'samalg'

  #120 opened a year ago by DinithiRajapaksha
  2

• UMAP looks like a line when neighborhood size was determined by using cell type labels

  #117 opened a year ago by Evenlyeven
  5

• The gene expression levels after SAMap-integrated are all greater than 0

  #116 opened a year ago by HYJ-hh
  2

• sankey_plot(MappingTable, align_thr=0.05, species_order = ['pl','sc','hy'])

  #100 opened 2 years ago by JoshuaNguyen123
  16

• How to use appropriate single cell data files as input files for SAMap correctly？

  #113 opened a year ago by HYJ-hh
  1

• SAMap and Docker

  #115 opened a year ago by avianalter
  2

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

  #114 opened a year ago by avianalter
  0

• SAMAP object instantiation fails with AttributeError

  #112 opened 2 years ago by carlosj-rr
  1

• Do noe know which reference should be choosen for doing blast

  #101 opened 2 years ago by houruiyan
  7

• AttributeError: type object 'object' has no attribute 'dtype'

  #110 opened 2 years ago by yangqi1999
  5

• Installation instructions in the README are wrong

  #111 opened 2 years ago by pnewstein
  1

• Converting files

  #103 opened 2 years ago by otoky
  2

• transfer_annotations - removed

  #104 opened 2 years ago by kullrich
  8

• Clarifying expression overlap plots

  #109 opened 2 years ago by dkeitley
  2

• Neighbourhood graph or embedding?

  #106 opened 2 years ago by YY-SONG0718
  2

• Running map_genes.sh

  #105 opened 2 years ago by wershofe
  2

• the dtype of array is not correct

  #107 opened 2 years ago by wubaosheng
  0

• "IndexError: boolean index did not match indexed array along dimension 0" in SAMAP call

  #102 opened 2 years ago by lb15
  6