Thread by @tangming2005

1/ 16 resources for re-analyzing public expression data.🧵

2/ RNA meta Analysis has ~26,700 studies (5,717 RNA-Seq and 20,955 Microarray)rnama.com/docs/search-ev…

3/ []() will have harmonized over 60,000 gene expression experimentsrefine.bio
refine.bio

4/ BioJupies maayanlab.cloud/biojupies/

5/ [Recount2-FANTOM]() Recounting the FANTOM Cage Associated Transcriptome. Long non-coding RNAs.biorxiv.org/content/10.110…

6/ Recount3 rna.recount.bio

7/ [dee2]() Digital Expression Explorer 2. Digital Expression Explorer 2 (DEE2) is a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive. By Ziemann Mark ! Version 2 of dee.dee2.io
et.al

8/ Extracting allelic read counts from 250,000 human sequencing runs in Sequence Read Archive biorxiv.org/content/10.110…

9/ [MetaSRA: normalized sample-specific metadata for the Sequence Read Archive]()biorxiv.org/content/early/…

10/ [ARCHS4: Massive Mining of Publicly Available RNA-seq Data from Human and Mouse]() ARCHS4 provides access to gene counts from HiSeq 2000, HiSeq 2500 and NextSeq 500 platforms for human and mouse experiments from GEO and SRA.amp.pharm.mssm.edu/archs4/

11/ [DEP-reads: Uniformlly processed public RNA-Seq data]() Read counts data for 5,470 human and mouse datasets from ARCHS4 v6 and 12,670 datasets from DEE2 for 9 model organisms by steven Ge.bioinformatics.sdstate.edu/reads/

12/ [SRA-explorer]() This tool aims to make datasets within the Sequence Read Archive more accessible.ewels.github.io/sra-explorer/

13/ [intropolis]() is a list of exon-exon junctions found across **21,504** human RNA-seq samples on the Sequence Read Archive (SRA) from spliced read alignment to hg19 with Rail-RNA.github.com/nellore/introp…

14/ [batch recompute ~20,000 RNA-seq samples from larget sequencing project such as TCGA, TARGET and GETEX](). Used `hg38` and `gencode v21` as annotation.genome-cancer.soe.ucsc.edu/proj/site/xena…

15/ [A cloud-based workflow to quantify transcript-expression levels in public cancer compendia]() used kallisto for TCGA/CCLE datasets and gencode v24 as annotation.biorxiv.org/content/early/…

16/ [MiPanda]() is an online resource for the interrogation and visualization of gene expression data from the myriad of publicly available cancer and normal next generation sequencing datasets.mipanda.med.umich.edu

17/ [Curation of over 10,000 transcriptomic studies to enable data reuse]()biorxiv.org/content/10.110…

18/ I hope you've found this tweet helpful.

Follow me @tangming2005 for more.

Subscribe to my youtube Channel

https://twitter.com/433559451/status/1805960457867624513

Enjoy this tweet? follow me @tangming2005 and join my newsletter to learn computational biology divingintogeneticsandgenomics.ck.page/newsletter