hic-te:master commitshttps://gitlab.fi.muni.cz/lexa/hic-te/-/commits/master2022-10-18T21:24:11+02:00https://gitlab.fi.muni.cz/lexa/hic-te/-/commit/8ff7320debd0f9c7ed110c8d12eaf7c3032fe61fChoice between RM and TE-nester added2022-10-18T21:24:11+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/fe74dade552d747bd46df4f6d7f8ec2f34966b9fFixed R script that complaint when no contigs were blasted and file had size ...2022-10-18T20:49:57+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/3df6c649c924b096bb7eb23da772cf41f56d0fcdFixed annotate_exons module grep problem, added promoters and enhancers to th...2022-10-18T20:22:50+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/525de20f01175105fca0b689a860c9168b31bfaaFixed annotate_exons module grep problem2022-10-18T20:14:43+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/c9ad68767be103be75d2c77078e6a5d316d09fa6Fied nextflow.config for human.config2022-10-18T19:44:42+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/9a3b9a47be1b6da29fcdbc1af1548813ab1d0503Merge branch 'master' of https://gitlab.fi.muni.cz/lexa/hic-te2022-10-18T19:29:42+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/0d8b04fcc294309feabfe2710eb7020cc3fe03b1Added human config2022-10-18T19:29:25+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/1c833f6f7187f2396e9df3404e4c599f984010acadded promoters and enhancers to annotate_exons.nf2022-10-12T20:23:58+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/5baee68fb7ec67ede81a8177e6bedbd2be27c77bfixed skip_sra2022-07-31T22:20:04+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/e3e744ce427b7faad20f44744fcb3148f20917a0Added empty variables for Repeat Masker option to test.config2022-06-09T16:06:10+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/6e2c0ca5127007baf29e2b0cfbdcaae03d95d9b7Added and tested repeat masker option on Arabidopsis2022-06-09T15:55:26+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/52eac3cbe49f97f9f62b5544291a25974d752339Added Repeat Masker notes and extra heatmap visualization parameters after ma...2022-06-07T09:15:58+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/6511372f4c1885681148dd3810341fa0db4e892dFixed a typo in the string reference_free that prevented printing heatmap cor...2022-06-02T19:23:55+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/e1368765af302c19c686dff71716eb40a0a8e730fixed bug in setting limit_count in heatmap plotting2022-06-02T17:32:15+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/edf114fcc71d76e2d9f30b2bb72e2328f8c17f2cLowere limit count from 50 to 30 and set it to 0 for reference-free2022-06-02T16:36:55+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/eea3937753477986b7c89d8578befb15baf9ac0eFixed a bug in bash skript choosing execution between nester and repeat masker2022-06-02T11:35:24+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/489948f455bede7843c4c2b9b0bcbd03fbc0c91bAdded statistical graying of heatmaps by two parameters for minimal read coun...2022-06-01T19:03:44+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/b45a6edcbcb3f53960e048be15d9eaa52d368a67A script to import RepeatMasker output2022-05-30T22:40:59+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/3a12d251f5886a60ff67649b3b40ef90d7a79a3fAdded a description of the counting procedure2022-05-19T08:46:27+02:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/590996c95d1021c4ea468055438f26053e68859dUpdate nester docker container2022-04-20T18:31:19+02:00Son Hoang Nguyenxnguyen3@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/0c99590a0f44e216f4b99b58a34a92bec246375fadded labels for track (family1 and family2), both families plotted separatel...2022-04-14T16:25:55+02:00Monika Čechováqmichal1@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/caa21d6f12312dca31f7df8dc4245d7f0eb4d4faMerge branch 'develop' into 'master'2022-04-14T16:14:20+02:00Matej Lexalexa@fi.muni.cz
Develop
See merge request <a href="/lexa/hic-te/-/merge_requests/1" data-reference-type="merge_request" data-original="lexa/hic-te!1" data-link="false" data-link-reference="false" data-project="18243" data-merge-request="34775" data-project-path="lexa/hic-te" data-iid="1" data-container="body" data-placement="top" title="Develop" class="gfm gfm-merge_request">!1</a>https://gitlab.fi.muni.cz/lexa/hic-te/-/commit/dddb7240e9f258f9adf4a7331d8d42c3a762e0b1Circos: gene densities and subsets of repeats are now plotted whenever possible.2022-04-14T14:32:02+02:00Monikacechova@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/ffab3b2db27d5e475a362f30768d500655865aa7Circos now plots gene track.2022-03-30T10:08:18+02:00Monikacechova@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/3bcaa3d93dc1b0bc6e61cc189fe490d57696a648Update Diachromatic.jar2022-03-21T16:24:04+01:00Son Hoang Nguyenxnguyen3@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/d71b3c1dab6cd3739de4de1e6dea6d7e7cfb1328Add files for building docker image for rtools2022-03-19T20:15:46+01:00Son Hoang Nguyenxnguyen3@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/8ff152926c63b45be7fbc4434135bdde346d2e28Fixed bin/R/plot_barplot.R to have wider margin below x-axis2022-01-04T15:28:35+01:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/5c99a833f5ae786697e5b251fe577518783a79e5Improved plantSat.fa description2022-01-04T14:58:17+01:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/b5f4fcf27245f49288e6bf51768fe6257266b47dAdded MIT license to the project root directory2022-01-04T14:51:20+01:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/da4941989576fda4d173dcf6a2b7d919f55d67e2Fixed bin/R/plot_barplot.R to widen with the number of families to show all l...2022-01-04T14:07:18+01:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/ccd95460660b1c683039d3dd290c347a0ea1d767clean scratch after the run2021-12-16T23:19:45+01:00Monika Čechováqmichal1@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/e0168722408503039d4cd9848d4bdea8bb036037Add new file2021-12-16T23:18:30+01:00Monika Čechováqmichal1@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/a0daa4ae09a17e213474f570955e3161df558f8euploading the test data for the arabidopsis into the local directory; later...2021-12-16T23:10:22+01:00Monika Cechovacechova@fi.muni.czuploading the test data for the arabidopsis into the local directory; later should be downloaded as part of the pipeline
https://gitlab.fi.muni.cz/lexa/hic-te/-/commit/b81d88d70ee047e346ab4ae886417b0b87636991Merge branch 'master' of https://gitlab.fi.muni.cz/lexa/hic-te2021-12-16T21:42:10+01:00Monika Cechovacechova@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/f585898f2ecc27ece9ebe207c12075fce7258084Modified the script for the metacentrum environment; sort redirected to /tmp2021-12-16T21:32:52+01:00Monika Cechovacechova@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/c64a1d9b2b6635622b6672f139a2928259bcc7b3Removed citation before URL of PlantSat in README2021-12-16T10:59:55+01:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/a9544b624e23132bd2b1416835553d3f15f30801Added URL to PlantSat in README2021-12-16T10:32:53+01:00Matej Lexalexa@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/9d94e466eb0978ea5885bdd02949056198bd1e12remove aggressive trimming of reads to be used for RepeatExplorer; only clust...2021-12-14T14:17:42+01:00Monika Čechováqmichal1@fi.muni.czhttps://gitlab.fi.muni.cz/lexa/hic-te/-/commit/f273c12023bd7f08a4695793b7efc7e716ed2e32make sure the chromosome names are trimmed after the first whitespace...2021-12-14T14:16:14+01:00Monika Čechováqmichal1@fi.muni.czmake sure the chromosome names are trimmed after the first whitespace (shouldn't be needed if upstream code is not changed)https://gitlab.fi.muni.cz/lexa/hic-te/-/commit/9101f7f1b78c9bb2cf747a0de3950048a7da0edesimplify how the genome files are calculated and remove the sequence after th...2021-12-14T14:14:23+01:00Monika Čechováqmichal1@fi.muni.czsimplify how the genome files are calculated and remove the sequence after the first whitespace for the chromosome names