sanjaynagi/rna-seq-pop

Issues

• error in rule DifferentialIsoformExpression when running test dataset - possible sleuth/R problem?

  #96 opened 12 days ago by azurillandfriend
  2

• variantanalysis in config should override other options

  #105 opened 12 days ago by sanjaynagi
  0

• move resources/regions to results

  #108 opened 12 days ago by sanjaynagi
  0

• increase freebayes version to 1.3.8

  #109 opened 12 days ago by sanjaynagi
  0

• provide singularity containers for the conda envs

  #91 opened a month ago by sanjaynagi
  0

• Change some config naming to make more sense

  #87 opened 4 months ago by sanjaynagi
  1

• qc_notebook requires fastp output

  #97 opened 4 months ago by sanjaynagi
  0

• allow local snpeff db

  #98 opened 4 months ago by sanjaynagi
  0

• matplotlib can't import docstring causes error in checkinputs

  #93 opened 10 months ago by azurillandfriend
  3

• remove venn diagrams

  #94 opened 10 months ago by sanjaynagi
  1

• xlsx and csv fail due to common.smk

  #86 opened a year ago by sanjaynagi
  0

• make isoform level DE optional

  #88 opened a year ago by sanjaynagi
  0

• fix single-end reads with column input

  #85 opened a year ago by sanjaynagi
  1

• In docs, do example analysis of bouake

  #62 opened a year ago by sanjaynagi
  0

• Allow .tsv or .xlsx or .csv metadata input

  #83 opened a year ago by sanjaynagi
  1

• Change syntax for contrasts

  #49 opened a year ago by sanjaynagi
  0

• Create Jupyter book and convert appropriate analyses to ipynb and papermill rather than py

  #77 opened a year ago by sanjaynagi
  2

• Configure conda envs so they work with conda channel priority = strict

  #81 opened a year ago by sanjaynagi
  0

• go on a code removal and tidying spree

  #76 opened a year ago by sanjaynagi
  1

• Problem installing the rna-seq-pop

  #43 opened a year ago by dieunelderilus
  6

• check codecov

  #59 opened 2 years ago by sanjaynagi
  0

• Make video tutorial/walkthrough

  #51 opened 2 years ago by sanjaynagi
  2

• Ensure meets FAIR principles and add to workflowhub.eu

  #78 opened 2 years ago by sanjaynagi
  0

• remove compkaryo and mpileup2readcounts submodules

  #65 opened 2 years ago by sanjaynagi
  1

• add venn and heatmap to documentation

  #58 opened 2 years ago by sanjaynagi
  1

• move gwss into different folders based on window size

  #73 opened 2 years ago by sanjaynagi
  1

• implement own gsea from GAF file

  #69 opened 2 years ago by sanjaynagi
  0

• rule that unzips a .fa.gz ref file

  #68 opened 2 years ago by sanjaynagi
  1

• add some resources directives

  #30 opened 2 years ago by sanjaynagi
  0

• add tests for main functions in rnaseqpoptools

  #60 opened 2 years ago by sanjaynagi
  0

• implement single-end read functionality

  #56 opened 2 years ago by sanjaynagi
  1

• Implement venn diagrams of expressed genes

  #50 opened 2 years ago by sanjaynagi
  1

• Implement heatmap script

  #52 opened 2 years ago by sanjaynagi
  0

• allowing custom snpEff databases

  #39 opened 2 years ago by vmkalbskopf
  4

• Change 'chrom' to 'contig'

  #40 opened 2 years ago by sanjaynagi
  1

• Implement Anopheles gambiae AIMs chromosome plot

  #45 opened 2 years ago by sanjaynagi
  0

• Adapting workflow to other species

  #38 opened 2 years ago by vmkalbskopf
  67

• change freebayes min depth param

  #42 opened 2 years ago by sanjaynagi
  2

• add CIs to Variants of interest module

  #41 opened 3 years ago by sanjaynagi
  1

• Check for signals.tsv

  #37 opened 3 years ago by sanjaynagi
  1

• allow fastq files to be specified in units.tsv

  #35 opened 3 years ago by sanjaynagi
  2

• remove need for DE contrasts rule

  #36 opened 3 years ago by sanjaynagi
  1

• Split regions by coverage

  #34 opened 3 years ago by sanjaynagi
  0

• add more options in config for everything

  #33 opened 4 years ago by sanjaynagi
  1

• progressiveDE - allow multiple groups comparisons

  #31 opened 4 years ago by sanjaynagi
  1

• split the genome into freebayes jobs of roughly equal size

  #32 opened 4 years ago by sanjaynagi
  1

• check that you can vary ploidy

  #28 opened 4 years ago by sanjaynagi
  2

• load individual packages instead of whole 'tidyverse'

  #29 opened 4 years ago by sanjaynagi
  2

• name all params and snakemake@ in scripts

  #27 opened 4 years ago by sanjaynagi
  1

• rename scripts

  #26 opened 4 years ago by sanjaynagi
  1