reg-gen
reg-gen copied to clipboard
CostaLab
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
IO read/write functions should be separated from the actual GRS. This will mean extracting all ```read_bed```, ```write_bed``` etc functions and putting them into Format classes that will take a GRS...
Hello RGT-HINT, I met error messages when running RGT-HINT footprinting: ```linux rgt-hint footprinting --organism mm10 --paired-end --output-location /mnt/e/HYJ/2022_7_23_ATAC-seq/results/RGT_HINT/ --output-prefix footprint_WT --atac-seq /mnt/e/HYJ/2022_7_23_ATAC-seq/results/bwa/mergedReplicate/control.mRp.clN.sorted.bam /mnt/e/HYJ/2022_7_23_ATAC-seq/results/bwa/mergedReplicate/macs/broadPeak/control.mRp.clN_peaks.broadPeak Report: The scikit HMM encountered errors when...
Hello, I have successfully ran RGT Hint to do differential transcription factor foot printing for ATACseq data. I am using RGT's HG38 human genome to align my data to, and...
 I encountered this error message when installing RGT. I noticed a warning when I ran the command "pip3 install RGT --no-binary RGT". It...
Hello! I tried running rgt-THOR on my data. Unfortunately, the it is not compatible with python 3.12, as the numpy dependency removed some necessary functions. Also i get quite some...
Hello. I have an issue during rgt-hint differential and it says: > Traceback (most recent call last): > File "/home/kthbecu/.local/bin/rgt-hint", line 8, in > sys.exit(main()) > File "/home/kthbecu/.local/lib/python3.10/site-packages/rgt/HINT/Main.py", line 95,...
Hi! I analyze ChIP-seq data between two conditions, 1 ChIP sample and 1 Input per each condition. I have some concerns about estimated extension sizes reported in *-setup.info. I obtained...
Hi! I call differentially enriched regions between two conditions: 1 ChIP sample per each and 1 Input sample per each. Besides p-values, I would like to obtain fold-change values between...
Where can I find instructions for results files? For example, the meaning of Protection_Score and TC in differential_statistics, and the meaning of the coordinate axis of the picture in Lineplots.
Hello I'm trying to run reg-gen on linux aarch64 server. unfortunatly provided libs.so are x86_64 ones I was abble to build librgt.so as the sources are provided, but `rgt-TDF` relies...
