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INSTALLATION
TUTORIALS
TUTORIALS
QUICK START
DDA-TMT
DDA-LFQ
DIA-LFQ
DE Analysis
PTM Processing
DDA-LFQ w. FlashLFQ
2024 Fulcher et al.
2024 Fulcher et al.
01 Process scRNAseq Data
02 Process Proteomics Data
03 Handle Multi-omics Data
HOW IT WORKS
HOW IT WORKS
Data
Filter
Normalization
Batch Correction
Summarization
Protein Inference
Precursor Isolation Purity
DE Analysis
Visualization
Command Provenance
API
API
read_h5mu
read_sage
read_diann
read_maxquant
read_fragpipe
read_sdrf
read_delpi
merge_mudata
preprocessing:
pp
preprocessing:
pp
add_filter
apply_filter
log2_transform
normalise
normalize
correct_batch_effect
to_peptide
to_protein
to_ptm
infer_protein
adjust_ptm_by_protein
scale_data
plotting:
pl
plotting:
pl
plot_correlation
plot_id
plot_intensity
plot_missingness
plot_pca
plot_umap
plot_upset
plot_var
tools:
tl
tools:
tl
compute_precursor_isolation_purity
compute_precursor_isolation_purity_from_mzml
pca
umap
corr
run_de
PermTestResult
StatTestResult
utils
utils
split_tmt
get_modality_dict
map_fasta
attach_fasta
get_label
uns_logger
append_cmd_log
add_quant
reindex_obs
select_repr_protein
parse_uniprot_accession
io
io
read_sage
read_diann
read_maxquant
read_fragpipe
read_sdrf
read_delpi
to_readable
write_csv
write_flashlfq_input
write_pin
setup_logger
setup_logger
Table of contents
setup_logger
Table of contents
setup_logger
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msmu.setup_logger