| #!/bin/bash | |
| # function Extract for common file formats | |
| function extract { | |
| if [ -z "$1" ]; then | |
| # display usage if no parameters given | |
| echo "Usage: extract <path/file_name>.<zip|rar|bz2|gz|tar|tbz2|tgz|Z|7z|xz|ex|tar.bz2|tar.gz|tar.xz>" | |
| else | |
| if [ -f "$1" ] ; then | |
| NAME=${1%.*} |
| id | name | type | class | released | |
|---|---|---|---|---|---|
| T01 | SupCar | toy | vehicle | yes | |
| T02 | SupPlane | toy | vehicle | no | |
| M01 | JeepX | model | vehicle | yes | |
| M02 | AircraftX | model | vehicle | yes | |
| M03 | Runner | model | people | yes | |
| M04 | Dancer | model | people | no |
| # --------------------------- | |
| # Accessing the material | |
| # https://tinyurl.com/bioc2017-ELMER | |
| # --------------------------- | |
| library("Bioc2017.TCGAbiolinks.ELMER") | |
| Biobase::openVignette("Bioc2017.TCGAbiolinks.ELMER") | |
| # --------------------------- | |
| # Section 1: | |
| # Aims: |
People
 :bowtie: |
😄 :smile: |
😆 :laughing: |
|---|---|---|
😊 :blush: |
😃 :smiley: |
:relaxed: |
😏 :smirk: |
😍 :heart_eyes: |
😘 :kissing_heart: |
😚 :kissing_closed_eyes: |
😳 :flushed: |
😌 :relieved: |
😆 :satisfied: |
😁 :grin: |
😉 :wink: |
😜 :stuck_out_tongue_winking_eye: |
😝 :stuck_out_tongue_closed_eyes: |
😀 :grinning: |
😗 :kissing: |
😙 :kissing_smiling_eyes: |
😛 :stuck_out_tongue: |
| url | name | user | type | |
|---|---|---|---|---|
| https://bioconductor.org/packages/regioneR | regioneR | NA | Bioconductor | |
| https://bioconductor.org/packages/karyoploteR | karyoploteR | NA | Bioconductor | |
| https://bioconductor.org/packages/metavizr | metavizr | NA | Bioconductor | |
| https://bioconductor.org/packages/IsoformSwitchAnalyzeR | IsoformSwitchAnalyzeR | NA | Bioconductor | |
| https://cran.rstudio.com/packages/UpSetR | UpSetR | NA | CRAN | |
| https://github.com/pachterlab/sleuth | sleuth | pachterlab | github | |
| https://github.com/nekrut/lab_site | lab_site | nekrut | github | |
| https://github.com/bernatgel/karyoploter_tutorial | karyoploter_tutorial | bernatgel | github | |
| https://bitbucket.org/biobakery/metaphlan2 | metaphlan2 | biobakery | github |
| "title" "gpl" "bioc_package" "manufacturer" "organism" "data_row_count" | |
| "Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I" "GPL15380" "GGHumanMethCancerPanelv1" "Illumina" "Homo sapiens" 1536 | |
| "Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)" "GPL8490" "IlluminaHumanMethylation27k" "Illumina, Inc." "Homo sapiens" 27578 | |
| "Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)" "GPL13534" "IlluminaHumanMethylation450k" "Illumina, Inc." "Homo sapiens" 485577 | |
| "GE Healthcare/Amersham Biosciences CodeLink™ ADME Rat 16-Assay Bioarray" "GPL2898" "adme16cod" "GE Healthcare" "Rattus norvegicus" 1280 | |
| "[AG] Affymetrix Arabidopsis Genome Array" "GPL71" "ag" "Affymetrix" "Arabidopsis thaliana" 8297 | |
| "[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array" "GPL198" "ath1121501" "Affymetrix" "Arabidopsis thaliana" 22810 | |
| "[Bovine] Affymetrix Bovine Genome Array" "GPL2112" "bovine" "Affymetrix" "Bos taurus" 24128 | |
| "[Canine] Affymetrix Canine Genome 1.0 Array" "GPL39 |