isoMiGA: Isoform and gene-level counts and TPM in short-read human microglia

https://github.com/RajLabMSSM/isoMiGA Isoform quantification performed with Salmon on 4 datasets from human microglia. Files are in the naming format {cohort}_{quantification}_{reference}.tsv.gz - 4 cohort, 4, quantifications, 2 references = 32 files. Cohorts: 1. Raj 350 samples from multiple brain regions. Publication PMID: 34992268 Raw data: https://dss.niagads.org/datasets/ng00105/ 2. Roussos 192 samples. Publication PMID: 35931864. Raw data: https://doi.org/10.7303/syn26207321 https://www.synapse.org/#!Synapse:syn52052829 3. Gaffney 118 samples. Raw data: https://ega-archive.org/datasets/EGAD00001005736 4. ipsc IPS-derived human microglia-like cells (iMGLs) 27 samples from 3 stimulation conditions. Citation: Navarro et al, LRRK2 G2019S variant triggers transcriptional changes in Parkinson’s disease human myeloid cells under pro-inflammatory environment, in preparation Raw data: Gene Expression Omnibus GSE240907 Quantification types: transcript_tpm: transcript-level quantification, TPM normalization transcript_counts: transcript-level quantification, estimated counts gene_tpm: gene-level quantification, TPM normalization gene_counts: gene_level quantification, estimated counts References: See https://zenodo.org/record/8290956 for details gencode: all transcripts in GENCODE v38: https://www.gencodegenes.org/human/release_38.html union: combination of all GENCODE v38 transcripts with 35,879 novel transcripts found in PacBio long-read RNA-seq