matsengrp/sumrep

Issues

• Install instructions need to be updated

  #46 opened 2 years ago by scharch
  0

• Using sumrep docker spec with singularity

  #44 opened 3 years ago by bcorrie
  0

• Dependencies missing in REDAME

  #42 opened 3 years ago by shashidhar22
  0

• compareRepertoires documentation needs to be updated

  #40 opened 5 years ago by scharch
  2

• Standardize locus input

  #30 opened 5 years ago by BrandenOlson
  1

• Error in rbindlist whilst running getPartisAnnotations

  #26 opened 5 years ago by Pezhvuk
  3

• libgfortran.so.4

  #10 opened 5 years ago by Pezhvuk
  7

• Error: `data` must be uniquely named but has duplicate elements

  #28 opened 5 years ago by Pezhvuk
  5

• Elaborate on IgBlast and ChangeO installation in docs

  #35 opened 5 years ago by BrandenOlson
  1

• Convert plotting functions to use plotUnivariateDistributions

  #39 opened 5 years ago by BrandenOlson
  0

• Getting indel statistics from IGBlast

  #38 opened 5 years ago by BrandenOlson
  0

• Clonal clustering for TCR repertoires

  #37 opened 5 years ago by BrandenOlson
  0

• Allow for general file extensions for IgBlast output

  #36 opened 5 years ago by BrandenOlson
  0

• Compute D gene summaries for TCR delta locus

  #34 opened 5 years ago by BrandenOlson
  0

• Check for correct object names in compareRepertoires

  #31 opened 5 years ago by BrandenOlson
  0

• Getting CDR3s from IGoR

  #19 opened 5 years ago by BrandenOlson
  1

• Error with partis

  #33 opened 5 years ago by Pezhvuk
  3

• Real-world data sets

  #18 opened 6 years ago by williamdlees
  21

• Allow custom filters in summaries of sequence columns

  #32 opened 5 years ago by BrandenOlson
  0

• partis command not passed to shell. while: Expression Syntax error.

  #23 opened 5 years ago by Pezhvuk
  2

• Summary plotting

  #11 opened 5 years ago by BrandenOlson
  2

• Output sequence length information for repertoire comparison

  #29 opened 5 years ago by BrandenOlson
  0

• -locus: invalid choice: 'ig'

  #24 opened 5 years ago by Pezhvuk
  2

• Safer column accessing

  #27 opened 5 years ago by BrandenOlson
  3

• improve Traceback calls

  #20 opened 5 years ago by Pezhvuk
  2

• AssignGenes.py is never called on one particular file when getIgBlastAnnotations is called

  #25 opened 5 years ago by Pezhvuk
  0

• Nearest_Neighbour error

  #21 opened 5 years ago by Pezhvuk
  11

• documentation - *running* sumrep

  #15 opened 5 years ago by scharch
  1

• Looser coupling to annotaters and simulators?

  #12 opened 5 years ago by williamdlees
  3

• Partis

  #22 opened 5 years ago by Pezhvuk
  4

• Definitions of mature and naive sequences

  #13 opened 6 years ago by BrandenOlson
  5

• Heavy/beta vs light/alpha chains

  #16 opened 6 years ago by BrandenOlson
  0

• Physicochemical features of CDRs

  #5 opened 6 years ago by BrandenOlson
  4

• Amino acid sequences?

  #14 opened 6 years ago by matsen
  3

• Distances between mutations on BCRs

  #4 opened 6 years ago by matsen
  1

• Joint/marginal VDJ usage distributions

  #3 opened 6 years ago by BrandenOlson
  0

• Extract per-gene-per-mutation rates from partis

  #1 opened 6 years ago by BrandenOlson
  1

• Automatic divergence averaging

  #7 opened 6 years ago by BrandenOlson
  2

• Comparing Substitution and Targeting Models

  #6 opened 6 years ago by BrandenOlson
  15

• Levenstein distance calculation

  #2 opened 6 years ago by matsen
  4

• Proportion of out-of-frame sequences

  #8 opened 6 years ago by BrandenOlson
  8