https://github.com/andrewdavidsmith/adssrc
A subset of the programs I use in my own data analysis.
https://github.com/andrewdavidsmith/adssrc
Last synced: about 1 month ago
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A subset of the programs I use in my own data analysis.
- Host: GitHub
- URL: https://github.com/andrewdavidsmith/adssrc
- Owner: andrewdavidsmith
- License: gpl-2.0
- Created: 2014-04-25T14:45:57.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2023-10-04T21:13:05.000Z (over 1 year ago)
- Last Synced: 2025-03-27T23:02:50.816Z (about 2 months ago)
- Language: C++
- Homepage:
- Size: 314 KB
- Stars: 3
- Watchers: 6
- Forks: 1
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
adssrc
======
Some of the code I use in my own data analysis. Some of this might
make it into smithlabcode repositories eventually.
collapsebed
-----------
This program takes a set of genomic intervals, and identifies each
maximal contiguous sub-iterval that overlaps a fixed number of the
input intervals. Then the set of sub-intervals overlapping more than
some specified number of the original intervals are reported.
majormethstate
--------------
The proagram looks at each "epiread" in an epiread formatted file (of
the kind used in amrfinder) and determines if the number of methylated
states in the read is lower than 0.5. If so, then the states are
inverted: all C changed to T, and all T changed to C. Then the epiread
is printed to a file or stdout. If you don't know why this might be a
useful thing to do, then you probably don't need to do it.
smoothmeth
----------
In methpipe the hmr program uses a 2-state HMM to identify
hypomethylated regions (HMRs) using a beta-binomial model for
emissions. This program takes the same approach for smoothing
methylation levels. Each of the 2 states has an average methylation
level, and the posterior probabilities for state occupancy at any CpG
site are extracted from the HMM. So if p is the posterior for being in
the high methylation state, and h is the methylation level for the
"high" state and l is the methylation level for the "low" state, then
the smoothed level is ph + (1 - p)*l. This program might eventually
replace how we build tracks for single-CpG methylation levels.
tsscpgplot
----------
I use this program to make meta-gene plots of methylation levels
around transcription start sites (TSS) but also around other fixed
landmarks in the genome. The program takes a BED format file, and
processes it in a stranded way, but currently it only works if the BED
interval is a single site, so the interval has size 1.