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AllonKleinLab / paper-data

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list of cells that used in figure 5 #4

Closed bioinformaticss closed 1 year ago

bioinformaticss commented 4 years ago

hey @calebweinreb @AllonKleinLab this is a really great work and I enjoyed reading it. In particular, figure 5 provides a good starting point for benchmarking RNA-seq fate prediction tools.

The process to get the cells was described in the paper but it is kind difficult to fully reproduce. And only the list of neutrophil cells in figure 5F are provided. Could you please also provide the complete list of cells that were used in figure 5A/B and 5C?

Thanks in advance and I am looking forward to hearing your replies!

calebweinreb commented 4 years ago

Hi,

A link to that list of cells is now on the website.

Also, I am attaching a folder with data and a notebook that is sufficient to fully reproduce the benchmarking analysis

On Mon, Jul 20, 2020 at 6:23 PM bioinformaticss notifications@github.com wrote:

hey @calebweinreb https://github.com/calebweinreb @AllonKleinLab https://github.com/AllonKleinLab this is a really great work and I enjoyed reading it. In particular, figure 5 provides a good starting point for benchmarking RNA-seq fate prediction tools.

The process to get the cells was described in the paper but it is kind difficult to fully reproduce. And only the list of neutrophil cells in figure 5F are provided. Could you please also provide the complete list of cells that were used in figure 5A/B and 5C?

Thanks in advance and I am looking forward to hearing your replies!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/AllonKleinLab/paper-data/issues/4, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABO45MW5J5EQYAACCBVQILTR4S7VNANCNFSM4PC3QA2Q .

bioinformaticss commented 4 years ago

thanks a lot for your quick reply! I am looking forward to the folder!

Btw, could you please also provide the names of the 10 genes that were included in fig5D (where only 3 TFs were shown)

calebweinreb commented 4 years ago

Hi, Here is a link to the folder for reproducing Fig. 5 https://www.dropbox.com/sh/zmst7q6tge5zneg/AABmYJwbPDbokPk4nKMOG3FJa?dl=0

The 10 genes were ['Pou2f2', 'Hdac9', 'Mef2c', 'Bcl6', 'Hlx', 'Zfp36', 'Satb1', 'Gata2', 'Ppp1r16b', 'Tle3']

On Wed, Jul 22, 2020 at 12:21 AM bioinformaticss notifications@github.com wrote:

thanks a lot for your quick reply! I am looking forward to the folder!

Btw, could you please also provide the names of the 10 genes that were included in fig5D (where only 3 TFs were shown)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/AllonKleinLab/paper-data/issues/4#issuecomment-662232501, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABO45MQBJ35H2LQV7IFHL5TR4ZSMHANCNFSM4PC3QA2Q .

bioinformaticss commented 4 years ago

That is awesome! Thank you for sharing the folder and the gene list.