cluster:73
Differences
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| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
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cluster:73 [2019/08/27 13:31] hmeij07 [Kallisto & Trinity] |
cluster:73 [2019/09/23 12:05] hmeij07 [R & R/parallel] |
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| ====== Kallisto & Trinity & FastQC====== | ====== Kallisto & Trinity & FastQC====== | ||
| + | |||
| + | **FastQC** A quality control tool for high throughput sequence data. | ||
| + | |||
| + | * '' | ||
| + | * location: / | ||
| + | * https:// | ||
| + | |||
| **kallisto** is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | **kallisto** is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | ||
| Line 379: | Line 386: | ||
| - | **FastQC** A quality control tool for high throughput sequence data. | ||
| - | * '' | ||
| - | * location: / | ||
| - | * https:// | ||
| ====== Sequencing Tools ====== | ====== Sequencing Tools ====== | ||
| Line 1822: | Line 1825: | ||
| ====== R & R/parallel ====== | ====== R & R/parallel ====== | ||
| + | * R 3.6.1 (running against " | ||
| + | * New java jdk-12.0.2 (by default in your path) | ||
| + | * packages lme4 and tidyverse installed (dependencies=TRUE) | ||
| + | * https:// | ||
| + | * packages: mice, rpart, party, caret(does not exist), randomforest, | ||
| + | |||
| + | < | ||
| + | |||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | |||
| + | #export PATH=/ | ||
| + | #export LD_LIBRARY_PATH=/ | ||
| + | |||
| + | </ | ||
| * R 3.5.1 (new libcurl package) | * R 3.5.1 (new libcurl package) | ||
| - | * Uses same old java home 1.7.0_21, should remember to update | + | * Uses same old java home 1.7.0_21 |
| * package lme4 installed | * package lme4 installed | ||
| Line 1833: | Line 1855: | ||
| export PATH=/ | export PATH=/ | ||
| export LD_LIBRARY_PATH=/ | export LD_LIBRARY_PATH=/ | ||
| + | |||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| </ | </ | ||
cluster/73.txt ยท Last modified: 2024/05/15 12:58 by hmeij07
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