-
Hi there, this is a bit of a shot in the dark, but I'm trying to wrap my head around analyzing broadPeak chip-seq files and stumbled across this repo. The approach described in https://github.com/resk…
-
- ChIP-Seq from own data
- ChIP-Seq SKNBE2
- ChIP-Seq Schödel
-
Jensen-Shannon Distance (JSD) plot
use deeptools npz output as input to jsd
encode: https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/master/src/encode_task_jsd.py
-
# About
Let's rename the `Input` column to `Input_Control` and make it an optional column (for ATAC-seq). The name `Input` for ChIP samples could causes some confusion for users who are not experie…
-
The dataset types in the gEAR portal are nice and tidy:
```
mysql> select dtype, count(dtype) from dataset group by dtype;
+-----------------------+--------------+
| dtype | coun…
-
IWC already contains a sufficient number of workflows that can be readily used for BRC purposes. We need to understands:
- understand which categories of workflows we have
- based on these categories…
-
Create a workflow for peak calling VISION ChIP-seq datasets that (as closely as possible) matches the ENCODE best practices pipelines. ENCODE pipelines are [here](https://github.com/ENCODE-DCC/chip-se…
-
It is not clear from docs if pileup support chip-seq tracks (narrow/broad peaks files). If yes, then it would be nice to see an example if no, then it would nice to know if the feature is in plans?
-
This paper looks really nice: https://doi.org/10.1093/nar/gkad1225
Has ChIP-seq, ATAC-seq, RNA-seq, enough replicates, two groups (for differential binding).
SRA: https://www.ncbi.nlm.nih.gov/b…
-
Hi,
could you tell me that which file in Stereo-seq data is or contains CID whitelist?
And when I get the CID barcode, how could I know the position in the chip?
Thank you !