matsengrp/phip-flow

Issues

• Migrate Dockerfile

  #78 opened 2 months ago by jgallowa07
  0

• streamlit phip-viz error on startup

  #71 opened 6 months ago by bkellman
  3

• sample_id not passed to aggregate

  #74 opened 6 months ago by bkellman
  5

• ALIGN:short_read_alignment (10) - ERROR

  #72 opened 6 months ago by martinezvbs
  2

• Low alignment

  #70 opened a year ago by bkellman
  4

• [improvement] Examples with summarize_by_organism

  #67 opened a year ago by bkellman
  1

• [possible bug] summarize_by_organism cannot find sample table

  #68 opened a year ago by bkellman
  12

• Unexpected behavior during nextflow run

  #66 opened a year ago by bkellman
  3

• Add documentation how to contribute.

  #62 opened 2 years ago by jgallowa07
  0

• BEER Analysis into workflow

  #56 opened 2 years ago by jgallowa07
  32

• gzip csv outputs

  #65 opened 2 years ago by jgallowa07
  0

• Fix broken images

  #61 opened 2 years ago by jgallowa07
  1

• update exmaple sample tables paths

  #64 opened 2 years ago by jgallowa07
  0

• Export `PhIPData` Object from pipeline

  #57 opened 2 years ago by jgallowa07
  1

• Deprecate or Remove Negative Binomial workflow

  #58 opened 2 years ago by jgallowa07
  0

• Remove automated output of binary

  #28 opened 2 years ago by jgallowa07
  0

• Add an automated test.

  #31 opened 2 years ago by jgallowa07
  0

• Model fitting subworkflow

  #35 opened 2 years ago by jgallowa07
  0

• batch-specific workflows

  #29 opened 2 years ago by jgallowa07
  0

• Add input checks

  #30 opened 2 years ago by jgallowa07
  0

• Integrating "phip-flow" command code directly into bin/

  #41 opened 2 years ago by jgallowa07
  0

• parse_config sub-workflow

  #42 opened 2 years ago by jgallowa07
  0

• Replicate Oligo nt Sequence Behavior

  #37 opened 2 years ago by jgallowa07
  4

• phip-flow command error when running merge-counts-stats.py

  #50 opened 2 years ago by dbayles
  6

• remove integer id requirement for sample and peptide table.

  #40 opened 3 years ago by jgallowa07
  1

• Merge seq_dir and fastq_filename

  #34 opened 3 years ago by jgallowa07
  0

• Multi-library Manifest

  #36 opened 3 years ago by jgallowa07
  3

• Move read, ad peptide length to config

  #32 opened 3 years ago by jgallowa07
  0

• Change the "file" type cast to "Path"

  #26 opened 3 years ago by jgallowa07
  0

• Document config files

  #24 opened 3 years ago by jgallowa07
  0

• DSL 2

  #21 opened 3 years ago by jgallowa07
  0

• Organize files

  #22 opened 3 years ago by jgallowa07
  0

• Make example dataset from Caitlin et. al. 2021

  #23 opened 3 years ago by jgallowa07
  0

• README Description of inputs and config

  #18 opened 4 years ago by jgallowa07
  0

• Quantify the impact of the library batch by comparing between tech and bio replicates

  #3 opened 4 years ago by matsen
  0

• Alignments stats

  #12 opened 4 years ago by jgallowa07
  0

• Re-factor the config setup.

  #15 opened 4 years ago by jgallowa07
  0

• Add automated simulation testing.

  #8 opened 4 years ago by jgallowa07
  1

• Local Alignment

  #11 opened 4 years ago by jgallowa07
  0

• Remove all non-relavent scripts.

  #13 opened 4 years ago by jgallowa07
  0

• Add more alignment schemes based on experiment type.

  #9 opened 5 years ago by jgallowa07
  0

• Restructure.

  #1 opened 5 years ago by jgallowa07
  0