idr
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nboley
IDR
README.md says ``` Get the current repo wget https://github.com/nboley/idr/archive/2.0.2.zip [...] Command Line Arguments [...] --use-best-multisummit-IDR Set the IDR value for a group of multi summit peaks (a group of peaks...
Hi, I have run IDR and looking at my output, trying to understand why I have peaks that are IDR < 0.05 ( based on column 11) yet the corresponding...
Hi, I performed IDR analysis on peaks called by MACS2 with the following command line: `idr --samples ${peakDir}/rep1_sorted_peaks.narrowPeak ${peakDir}/rep2_sorted_peaks.narrowPeak \ --input-file-type narrowPeak \ --rank p.value \ --output-file regular_model-idr \ --plot...
Hi, I run idr with the test narrowPeaks files and my own narrowPeaks files. They all ended up with an error: [wszheng@guru idr-2.0.2]$ idr --samples tests/data/peak1 tests/data/peak2 WARNING: Cython does...
Hi, I've successfully installed idr in my linux server. When I call idr from command line in the idr-2.0.2/ path, it's fine, but when call idr in other path, I...
It seems that the argument `--use-nonoverlapping-peaks` is never used. Instead, the code checks for an argument "--use_nonoverlapping_peaks". When I corrected this and ran it on two replicates where there are...
I ran IDR on the list of peaks where some of the summit values are -1, and I got the following error: > File "/mnt/silencer2/home/yanxiazh/.local/lib/python3.4/site-packages/idr-2.0.3-py3.4-linu x-x86_64.egg/idr/idr.py", line 222, in merge_peaks_in_contig...
Hi, Does anyone know how to uninstall idr on a MAC OS X? Cheers, Ben
For certain histone modifications, [ENCODE uses the gappedPeak representation.](https://sites.google.com/site/anshulkundaje/projects/encodehistonemods) Right now IDR doesn't support using gappedPeak files - is there a workaround for this? For example, converting a gappedPeak file...
Hi Nathan, I am wondering if the IDR can be installed on windows 7. Is there a way that I can follow for a smooth installation. ajeet
