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Dear all,
Thank you for developing LINGER.
I am trying LINGER with different metacells inputs and I could successfully infer different cell population gene regulatory networks for each of them.
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### Task motivation
Gene Regulatory Network (GRN) inference is pivotal in systems biology, offering profound insights into the complex mechanisms that govern gene expression and cellular behavior. Th…
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Hi LINGER team,
paper looked really cool! So wanted to try and run on some of my own data and tried to download the general GRN using the wget code provided:
`wget --load-cookies /tmp/cookies.txt …
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--Brian has implemented scripts to compute GRNs, score each cell for the activity of GRNs, created tSNE visualizations of these networks with Scanpy, which look very good, and calculated enrichment of…
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when I try the Gene Regulatory Networks tutorial , the first step "results.ctl=compute.network(expr.data = expr.ctl,gene.names = gene.names)" reported an error:
Error: 'rowSort' is not an exported ob…
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The required cisTarget databases and scripts to construct gene regulatory network can be downloaded [here](https://
figshare.com/articles/dataset/Auxiliary_data_and_codes_for_scPlant/23498402),but th…
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Thank you for providing such high-quality resources. As referenced in the supplementary data of the article, I am seeking a more detailed methodology for constructing GRNs (e.g., metacell, GRN evaluat…
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I ran CreateNetwork on a batch of " _bound.bed" files and got
1. adjancent.txt
2. edges.txt
3. a paths and edges file for each TF for which inputted the bed file.
The edges.txt file output is a…
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KINC outputs a "tidy" network that has edges containing two genes. Gene 1 is a "Source" edge and gene 2 is a "Target" edge.
The labels "Source" and "Target" imply causality, but KINC is not capable…
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Hello, thank you for your convenient tools. I want to only focus on TFs regulating a exact set of genes and construct regulatory network on it. How can I do it? Is it right to use gene sets tpms expre…