tanaylab/metacells

Issues

• Updates

  #58 opened a year ago by orenbenkiki
  3

• broken links in the vignette

  #75 opened a month ago by onurcanbektas
  2

• convert MC to Seuratobject format

  #72 opened 3 months ago by jadewu77
  5

• Rare genes, rare cells, and outliers in divide and conquer

  #74 opened 3 months ago by LoaiNaom
  4

• How to pick the lateral genes ?

  #73 opened 3 months ago by LoaiNaom
  6

• ctx pyscenic Error

  #71 opened 4 months ago by angelica-varesi
  1

• metacells2 'unknown mask data: lateral_gene'

  #70 opened 4 months ago by angelica-varesi
  4

• divide_and_conquer_pipeline Error

  #69 opened 4 months ago by simonekats
  7

• mc.pl.extract_clean_data(full, name="hca_bm.one-pass.clean") crashes jupyter notebook everytime

  #66 opened 7 months ago by lindsdudley
  19

• Format error

  #65 opened 9 months ago by Ray569743422
  1

• How can I save meta cells and its gene count as a txt file?

  #64 opened 9 months ago by jrahimik
  6

• Meaning of aggregated values in metacells

  #63 opened 10 months ago by annaKett
  3

• Preserving a reasonable number of rare cells

  #62 opened 10 months ago by annaKett
  6

• Is there a way to automate this pipeline?

  #61 opened a year ago by crotoc
  5

• Define number of Metacells

  #60 opened a year ago by antonio-miranda
  1

• _collect_metacell() performs unweighted geomean for regularization values

  #59 opened a year ago by orenmn
  1

• to_proper_matrix doesn't transform the layout of compressed matrices

  #57 opened a year ago by ukleiner
  1

• downsample_cells asserts for "float32" type, prohibits "float64"

  #56 opened a year ago by ukleiner
  1

• [compilation not working] install option native not found

  #44 opened a year ago by blackTay
  1

• Adding forced genes to feature genes in divide_and_conquer_pipeline

  #46 opened a year ago by orimosko
  1

• Divide and conquer issue

  #55 opened a year ago by SalimMegat
  9

• Key error "clean genes"

  #54 opened a year ago by SalimMegat
  2

• Assertion error

  #53 opened a year ago by SalimMegat
  2

• scipy.sparse.compressed error

  #23 opened a year ago by rargelaguet
  3

• Create layer of per-cell summed UMIs into the MC

  #26 opened a year ago by orenbenkiki
  2

• Metacells analysis gets killed in divide_and_conquer_pipeline

  #31 opened a year ago by aschlicker
  4

• Why do i got ValueError: Empty feature data, giving up

  #33 opened 2 years ago by chansigit
  2

• compute_for_mcview() computes gene-gene similarity without normalization

  #34 opened a year ago by orenmn
  2

• _compute_elements_similarity() might return wrong correlation values

  #35 opened a year ago by orenmn
  3

• QC Metrics

  #43 opened a year ago by AlexAdrian-Hamazaki
  2

• noisy genes can be selected for computing similarity

  #49 opened a year ago by orenmn
  1

• vignettes for 0.8

  #52 opened a year ago by GabyBG
  2

• Parallelization of some QC routines overloads the system

  #24 opened 2 years ago by tzeitim
  34

• compute_for_mcview doesn't add mcview_format

  #51 opened a year ago by ukleiner
  3

• Thread explosion

  #50 opened a year ago by sophie-xhonneux
  1

• Metadata Attribution for scRNAseq Metacells

  #45 opened a year ago by fadichoucha
  3

• No explaination for AttributeError in mc.pl.divide_and_conquer_pipeline

  #42 opened 2 years ago by zvittorio
  2

• AttributeError: partially initialized module 'metacells' has no attribute 'ut'

  #38 opened 2 years ago by imet-k
  4

• Annotate metacell obs information

  #37 opened 2 years ago by Sayyam-Shah
  2

• Metacell count matrix

  #36 opened 2 years ago by Sayyam-Shah
  5

• AssertionError on outgoing rank from KNN

  #30 opened 2 years ago by Benfeitas
  3

• Negative metacells

  #32 opened 2 years ago by Sayyam-Shah
  1

• AssertionError related with parallelization in divide_and_conquer_pipeline

  #29 opened 2 years ago by Benfeitas
  4

• enforcing metacells by donor

  #28 opened 2 years ago by hoondy
  4

• Migrate to daf

  #27 opened 2 years ago by orenbenkiki
  0

• pip installation of MC2 can misdirect BLAS library paths

  #25 opened 2 years ago by tzeitim
  1

• Would like to use harmonized PC as input to minimize batch effect

  #22 opened 3 years ago by hurleyLi
  5

• actual cells behind a metacell

  #21 opened 3 years ago by chansigit
  1

• analyze_clean_genes small bug?

  #20 opened 3 years ago by hurleyLi
  2

• Keep track of cell barcodes that end up in a metacell

  #19 opened 3 years ago by tzeitim
  1