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remove_proteins_by_name()now has some more flexibility for filtering undesired proteins from input, e.g. proteins from known contaminants/crapome FASTA. -
differential_detection_filter()is a new function for finding/filtering proteins that are detected in N samples in one sample ground and with less than M samples in another sample group. It also includes a cutoff/threshold for the ratio of detected peptides (per protein, across all samples) between sample groups. -
importing FASTA files now replaces semicolon symbols in headers with colons because we use semicolons as delimiter symbols (only recently have semicolon symbols been appearing in uniprot FASTA files, e.g.
>tr|B1AR09|B1AR09_MOUSE Isoform of B1AR10, Myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6 OS=Mus musculus OX=10090 GN=Mllt6 PE=1 SV=1) -
bugfix for plotting Cscore histograms in Spectronaut datasets to deal with samples that contain very few observed peptides
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bugfix for "differential detection" to deal with datasets that contain any sample with 0 detected peptides
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bugfix for reducing the RAM and RData footprint of large Spectronaut datasets