archs4

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CPM and TPM from gene_abundance.tsv

1

Hi, In issue https://github.com/MaayanLab/archs4/issues/30, you shared how to obtain gene abundance values from the transcript expression levels. I would like to know how to obtain CPM and TPM values from...

malonzm1

[Question]: License page clarificaion

2

Hi @AviMaayan and @lachmann12 Thanks for the work here. I read through the license page - https://github.com/MaayanLab/archs4/blob/master/LICENSE and I am not clear if say utilities like [gget](https://github.com/pachterlab/gget) can be used...

tamuanand

ENSG genes when using gene_symbols

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Hi, When I use the R script (h5read(destination_file, "meta/genes/gene_symbol")) the matrix generated includes genes with prefix ENSG along with regular gene symbols. Why is this? Thanks and good day.

malonzm1

Hi again, When I upload a fastq.gz file to elysium from a server (tunneled via SMB), I get the following error: RequestTimeoutYour socket connection to the server was not read...

malonzm1

Hi, Why are the gene counts from elysium in float format whereas the gene counts from archs4 in integer? Thanks.

malonzm1

Hi, I have about 700+ fastq files (16 GSE IDs) I would like to submit to get gene expression files. Is there a way for me to programmatically do this...

malonzm1

Latest pipeline to create ARCHS4 Version 2.1.2 h5 files?

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Hi, What is the pipeline used to create human_matrix_v2.1.2.h5 and mouse_matrix_v2.1.2.h5 ? Is it the same as the pipeline mentioned in the 2018 paper? Thanks.

seraphzl

When I download an R script to read gene expression data for human data, the initial variables are as follows: destination_file = "human_matrix_v10.h5" extracted_expression_file = "GSE30017_expression_matrix.tsv" url = "https://s3.amazonaws.com/mssm-seq-matrix/human_matrix_v10.h5" I...

jasonhan3

Duplicate Gene Names Implications?

1

hi @lachmann12. I really appreciate this resource , it is truly great help. But apparently I noticed [this]( https://github.com/MaayanLab/archs4/issues/38#issue-2106403213) too and as you may see in the screenshot attached that...

amnahsiddiqa

human_gene_v2.5.h5 fails file integrity check

3

Not an issue with the GH repo per say, but I noticed that the latest ARCHS4 file for human gene expression (human_gene_v2.5.h5) fails a file integrity check. Reproduce: ```bash wget...

wigginno