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## Hierarchy of RE
```
LTR (Family) —> L1 (Sub-Family) —> L1_Rod (Gene) —> L1_Rod_dup1 (Transcript)
LTR (Family) —> L1 (Sub-Family) —> L1_Rod (Gene) —> L1_Rod_dup2 (Transcript)
LTR (Family) —> L1 …
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In [ATAC-seq/auyar/](https://github.com/TheJacksonLaboratory/ATAC-seq/tree/master/auyar), there are a number of bash shell scripts (`*.sh`) that need to be unified with the workflow described by auyar…
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- [x] mRNAseq DESeq2
- [ ] mRNAseq sleuth
- [ ] noncoding RNAseq
- [ ] WGBS
- [ ] ATAC-seq
- [ ] ChIP-seq
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### Description of feature
This issue is to provide an overview of different tools and related sub-issues related to supporting multiple modalities:
- CITE-seq (=RNA+protein) (https://github.co…
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This is a question about the .table file. I understand that LIGER integrates the scATAC and scRNA-seq. What exactly does this .table contain, and how can I generate it from other pipelines (Seruat, sc…
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Hi,
I am trying to use msCentipede on a ATAC-seq time course series without success. I get an error when running a command like
python call_binding.py --task learn --protocol ATAC_seq testbk/Ctcf_…
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Hello,
Thanks for this very useful package!
I just have a few questions after runnning on single-cell ATAC-Seq libraries generated from the 10X multiome kit. I ran using the following commands:
…
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Dear respected author,
Hello! I am thrilled and deeply inspired after reading your work, as I am currently seeking methods to distinguish diploid and tetraploid cells in plant scRNA-seq data. I w…
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I have bulk ATAC-seq from two cell populations (two replicates each). Papers suggest for bulk counts to apply quantile normalization followed by GC bias normalization using CQN.
Does chromVAR acco…
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> cat PUMATAC_tutorial-main/PUMATAC/src/singlecelltoolkit/processes/barcode_correction.nf
nextflow.enable.dsl=2
//binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/singlecelltoolk…