BIOPM helper scripts

Small helper scripts for data transformation and analysis

List of scripts:

1. convertEdgeRcsv.py: read in miRNA counts <hairpin/mature>_counts.csv file from nf-core/smrnaseq, and converts it to merged_gene_counts.tsv as input run rnadeseq. Requires a*
2. convertMirge3Counts.py: read in miRNA counts mir.Counts.csv output file from mirge3 workflow, and converts it to merged_gene_counts.tsv as input to run rnadeseq. Requires a*
3. filterSalmon.R: to filter salmon files (quant.sf and quant.genes.sf) for genes, which were called DE using DESeq2 in qbic-pipelines/rnadeseq, but are extremely low expressed and cause wings in Volcano plots (see for example here: https://x.com/bioinformer/status/1570103140741152768).
   The script has 4 positional arguments:
   [1] The Salmon folder as one of the main result folders of nf-core/rnaseq in the style of "star_salmon/QbiCBarcode"
   [2] The final DE table from the results folder of qbic-pipelines/rnadeseq, usually named "final_DE_gene_list.tsv"
   [3] The baseMean value to filter for (genes with baseMean < this value will be removed from [1]
   [4] Metadata file from the results folder of qbic-pipelines/rnadeseq, usually named "metadata.tsv"
   [5] The tax2gene tsv file from the Salmon folder of a nf-core/rnaseq run, usually named "salmon_tx2gene.tsv"
   Typical command to run and log the process is:
   Rscript filterSalmon.R star_salmon final_DE_gene_list.tsv 5 metadata.tsv salmon_tx2gene.tsv 2>&1 | tee filterSalmon.log

Notes:

1. a*: an environment running python3 with packages pandas installed.