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assets/annotation_tools.tsv

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+Tool	Description	Pros	Cons
+**[org.Xx.eg.db](https://bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.pdf)**	Query gene feature information for the organism of interest	gene ID conversion, biotype and coordinate information	only latest genome build available
+**[EnsDb.Xx.vxx](http://bioconductor.org/packages/devel/bioc/vignettes/ensembldb/inst/doc/ensembldb.html)**	Transcript and gene-level information directly fetched from Ensembl API (similar to TxDb, but with filtering ability and versioned by Ensembl release)	easy functions to extract features, direct filtering	Not the most up-to-date annotations, more difficult to use than some packages
+**[TxDb.Xx.UCSC.hgxx.knownGene](https://bioconductor.org/packages/release/bioc/vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf)**	UCSC database for transcript and gene-level information or can create own *TxDb* from an SQLite database file using the *GenomicFeatures* package	feature information, easy functions to extract features	only available current and recent genome builds - can create your own, less up-to-date with annotations than Ensembl
+**[annotables](https://github.com/stephenturner/annotables)**	Gene-level feature information immediately available for the human and model organisms	super quick and easy gene ID conversion, biotype and coordinate information	static resource, not updated regularly
+**[biomaRt](https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html)**	An R package version of the Ensembl [BioMart online tool](http://www.ensembl.org/biomart/martview/70dbbbe3f1c5389418b5ea1e02d89af3)	all Ensembl database information available, all organisms on Ensembl, wealth of information	

assets/gsea_Cont-Vamp_kegg.csv

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+,ID,Description,setSize,enrichmentScore,NES,pvalue,p.adjust,qvalue,rank,leading_edge,core_enrichment
+hsa03040,hsa03040,Spliceosome,139,0.721217720563705,2.28166468380881,1e-10,3.39e-08,2.92631578947368e-08,1565,tags=20%, list=8%, signal=19%,124904135/124904136/124904137/124904138/124904139/124904140/124904141/124904142/124904143/124904144/124907963/124907964/124907965/10262/6634/6631/9939/220988/8683/9129/151903/3312/2521/84321/24148/4809/57819/84991
+hsa05322,hsa05322,Systemic lupus erythematosus,119,-0.60772756530301,-1.93280553556629,1.15068424169896e-05,0.00195040978967974,0.00168363273259111,1326,tags=22%, list=6%, signal=21%,8348/8353/3586/8347/440689/8970/92815/7124/8358/8336/942/1991/718/8343/8357/723790/8341/8349/128312/8329/8344/940/8360/3017/8367/8370
+hsa04613,hsa04613,Neutrophil extracellular trap formation,172,-0.534369615216681,-1.78908867037288,2.48693906725814e-05,0.00220821755714886,0.00190617755282528,1394,tags=19%, list=7%, signal=18%,3689/51284/8348/1183/8353/8347/7450/440689/8970/92815/6403/8358/1432/8336/2243/2266/1991/718/8343/8357/5330/723790/23569/8341/8349/128312/3683/8329/8344/8360/3017/8367/8370
+hsa05168,hsa05168,Herpes simplex virus 1 infection,452,-0.41947353763512,-1.54404104662865,2.6055664391137e-05,0.00220821755714886,0.00190617755282528,3530,tags=37%, list=17%, signal=31%,139735/388561/110116772/6428/256051/1978/10379/146434/55552/84503/91664/7700/199777/7582/7728/10793/126375/7712/57693/6773/125919/90576/7189/7565/7297/5371/342908/146540/7574/65243/90317/3122/374928/7639/147694/9668/57335/7556/7773/54811/7699/3678/7772/567/170959/7695/55713/147948/7766/80110/58492/163087/390927/125893/7576/126068/339327/5610/388566/22835/6432/284390/285268/84911/400713/79724/79862/329/9831/3105/90321/147949/388567/54807/201514/8772/1147/3115/7710/284309/84527/163227/90592/340252/163049/8892/26974/84436/7638/57547/348327/90594/6892/9534/641339/972/10929/6347/29915/83744/7767/7594/148203/9310/219749/51427/7711/10224/197320/90075/65251/7770/57677/148103/4792/57232/7769/94039/374900/168374/7617/64135/7644/101060200/284370/126070/93474/7637/9451/7752/7768/92285/7124/374879/7673/729747/92283/10308/728927/147657/7554/80778/388536/284349/342909/84765/163081/162655/7539/7561/147923/284307/10520/718/152687/199692/148254/10795/155054/55659/3135/10794/163059/3593/10172/79973
+hsa05022,hsa05022,Pathways of neurodegeneration - multiple diseases,415,0.428436010791993,1.53330432078322,6.91690928768895e-05,0.00468966449705311,0.00404821217258427,4202,tags=37%, list=20%, signal=30%,2902/1769/598/4541/25981/81029/55567/1536/4539/4519/5970/2878/11211/50507/2776/5608/11047/4747/7415/7345/2932/22943/9776/572/7332/5664/22863/4893/1020/5532/818/4726/356/84516/8312/10010/120892/10105/5709/4720/4722/7326/3845/3552/581/2521/355/5599/808/3569/3265/5578/4702/7473/23236/578/1857/5609/5715/26100/5708/488/4514/5701/8851/81027/203068/2475/5707/11315/5692/27035/4725/5702/8322/1855/5705/5602/7477/3553/10131/324/5704/1131/79139/1139/4707/5071/4717/5687/6647/5691/8408/4718/54361/8678/55860/9861/7311/8326/836/3064/4723/317/9377/805/5606/9927/64837/126328/4728/11258/3799/10671/515/5714/7419/4715/10121/51465/516/4713/9217/514/5684/1459/4696/29982/5335/292/369/1329/4716/842/1349/5603/5706/7327/10376/5689/27429/4710/201625/1460/5481/513/518/4694/10297/776/23435/5663/5683/5682/1337
+hsa05014,hsa05014,Amyotrophic lateral sclerosis,302,0.45125917417916,1.56725962653071,0.000149338624631757,0.00843763229169426,0.00728353292063656,4922,tags=43%, list=24%, signal=34%,2902/1769/598/4541/25981/55567/4539/4519/2878/60/5608/11047/4747/7415/9776/572/22863/5532/4726/84516/10010/220988/5709/4720/4722/581/2521/10482/4702/5903/5715/26100/311/5708/4514/5701/81027/203068/2475/5707/5692/81929/3178/4725/5702/79902/5705/10762/5704/79139/4707/55916/5071/4717/5687/6647/5691/4686/8408/4718/8678/55860/9861/836/4723/317/9377/5606/64837/126328/4728/11258/3799/10671/515/5714/4715/10121/516/4713/9217/514/5684/283/4696/29982/1329/4716/842/1349/5603/129401/5706/6396/100101267/10376/5689/9972/4710/201625/513/518/4694/8480/29979/55746/23435/5683/5682/1337/10476/5718/596/9688/1537/55967/23064/51079/9818/3800/57122/23165/506/2876/7186/2891/1965/1351/10718/51807/25978
+hsa05010,hsa05010,Alzheimer disease,336,0.426014891538371,1.49592374715327,0.000270905069698274,0.013119545518245,0.0113250540415218,4306,tags=40%, list=21%, signal=32%,2902/4541/81029/1536/4539/4519/5970/11211/50507/2776/11047/2932/22943/5295/9776/572/5664/22863/4893/4311/1020/5532/4726/55851/8312/10105/5709/4720/4891/4722/3845/3552/355/5599/808/3569/3265/4702/7473/23236/1857/5609/5715/26100/5708/488/4514/5701/8851/81027/203068/2475/5707/5692/27035/4725/5702/8322/1855/5705/5602/7477/3553/23516/324/5704/1131/1139/64116/4707/4717/5687/5691/8408/4718/54361/8678/9861/8326/836/4723/317/9377/805/5293/91252/64837/10313/126328/4728/8517/3799/515/5714/7419/4715/516/4713/55334/4035/514/5684/1459/4696/3630/29982/8503/292/369/1329/4716/842/1349/5706/10376/5689/29985/4710/1460/5481/513/207/518/4694/8660/10297/776/5663/5683/5682/1337/8883/10476/5718
+hsa05016,hsa05016,Huntington disease,263,0.444627945085508,1.52507259654836,0.000339460247800036,0.0143846280005265,0.0124170985379487,4918,tags=47%, list=24%, signal=36%,2902/1769/4541/25981/55567/4539/4519/2878/2776/11047/9776/5439/22863/5434/4726/84516/10105/5709/4720/4722/5438/581/548644/5599/3065/4702/23236/5609/5715/26100/5708/10488/4514/5701/81027/203068/2475/5707/7019/5692/4725/5702/5705/5602/1175/5704/1211/4707/4717/5687/6647/5691/8408/4718/1173/8678/55860/9861/836/3064/4723/317/9377/64837/126328/4728/11258/3799/10671/515/5714/7419/4715/10121/516/4713/514/5684/4899/4696/29982/292/1329/4716/842/5432/1349/5706/10376/5689/6908/4710/201625/1212/5433/513/5431/518/4694/161/5683/160/1387/5682/6648/1337/5468/10476/5718/1537/5437/55967/51079/3800/506/2876/7186/6874/5440/2891/1351/51807/841
+hsa05020,hsa05020,Prion disease,223,0.46236545791933,1.56258534302751,0.000582728614207916,0.0219494444684982,0.0189471993859416,4306,tags=41%, list=21%, signal=33%,2902/4684/4541/1536/4539/4519/11047/2932/5295/1958/5566/572/5880/5532/4726/10105/5709/4720/4722/3552/3312/581/5599/3569/4702/5715/5708/6352/10488/4514/5701/81027/203068/5707/5692/4725/5702/5705/5602/3553/5704/4707/857/1535/4717/5687/6647/5691/4718/9861/836/4723/317/9377/5293/64837/126328/4728/3799/515/5714/7419/4851/4715/516/4713/514/5684/1459/4696/8503/292/1329/4716/842/1349/5603/5706/10376/5689/4710/1460/513/518/4694/1388/776/5683/5682/1337/10476/5718
+hsa00190,hsa00190,Oxidative phosphorylation,113,0.536635404947576,1.66711623822259,0.000783491452752456,0.0241457820439166,0.0208431219009744,4680,tags=45%, list=23%, signal=35%,4541/4539/4519/528/9550/535/4726/4720/4722/9551/4702/9296/4514/537/523/10063/4725/4707/4717/4718/526/10632/4723/9377/126328/4728/515/4715/516/4713/533/514/8992/1352/4696/1329/4716/1349/521/51606/4710/513/518/4694/1337/10476/1537/55967/51079/51382/506
+hsa05034,hsa05034,Alcoholism,171,-0.473290473379284,-1.58309727117715,0.000727569001230357,0.0241457820439166,0.0208431219009744,1672,tags=18%, list=8%, signal=16%,91860/126961/2906/53358/8348/8353/8347/2786/440689/8970/92815/9586/8358/2792/8336/64764/8343/8357/25759/627/723790/8341/8349/128312/8329/8344/8360/3017/8367/8370
+hsa05200,hsa05200,Pathways in cancer,491,0.383512522080713,1.39424740952262,0.00104455602914826,0.0295087078234383,0.0254725066757207,2821,tags=29%, list=14%, signal=26%,598/6772/405/81029/7187/1436/2308/3439/2952/5970/4312/2353/4616/2736/11211/1612/2776/2147/3561/2932/2885/5295/6934/8900/5566/7015/3565/6513/572/2122/6776/2782/675/5914/9915/896/2768/3559/4893/5880/26508/1870/79444/998/3568/818/3574/356/107/332/5155/1910/6258/5888/8312/7170/3718/6257/5467/2944/6469/23566/1488/3845/9134/581/4318/3458/6688/2099/355/5599/808/3065/3569/3265/5578/7424/7473/23236/578/238/1857/1050/3716/4087/5925/4292/330/2034/2335/7296/4914/6777/387/4853/2263/2057/7185/2475/861/25/59345/1487/3595/3480/7046/8322/5915/2324/2261/3594/4233/1855/5602/7477/10672/324/3479/4149/3674/6387/890/898/3560/7704/2791/999/6500/54361/9618/4313/3326/26060/2322/2264/8326/8030/836/2846/317/3082/805/5293
+hsa03050,hsa03050,Proteasome,37,0.687215523613715,1.79064624810197,0.00137003412196073,0.0345329638348401,0.0298095449342821,4306,tags=70%, list=21%, signal=56%,5699/11047/5709/3458/10197/5715/5708/5701/5707/5692/5702/5705/5704/5687/5691/9861/9491/5714/5684/23198/5706/5689/5683/5682/51371/5718
+hsa05208,hsa05208,Chemical carcinogenesis - reactive oxygen species,198,0.45301674962014,1.50210782805316,0.00147485398950266,0.0345329638348401,0.0298095449342821,3990,tags=38%, list=19%, signal=31%,405/4541/9020/2952/4539/4519/5970/1571/2353/50507/2885/5295/572/196/4893/5781/4726/10105/2944/4720/4722/3845/5599/3265/4702/5609/65010/6714/4514/25/27035/4725/4233/5602/2309/4707/1535/6416/4717/6647/4718/52/4723/1545/3082/9377/5293/126328/4728/8517/515/7419/4715/516/4713/1950/514/4696/23683/8503/292/369/1329/4716/1349/5603/9446/119391/5747/4710/513/7422/207/518/4694
+hsa04060,hsa04060,Cytokine-cytokine receptor interaction,259,-0.419843445205899,-1.46979365216371,0.00152800724932921,0.0345329638348401,0.0298095449342821,1362,tags=20%, list=7%, signal=19%,6347/3566/1440/7852/939/51554/6362/7066/3586/6356/3601/3579/944/7048/3953/1234/650/130399/9466/2056/8794/27242/7040/60401/7124/3952/4803/2661/1435/7133/4838/3626/3625/4982/6364/1271/9518/6366/3576/3562/6363/8795/1441/6367/64109/3593/3567/8743/115650/1236/50615
+hsa00983,hsa00983,Drug metabolism - other enzymes,62,0.602089840988985,1.69612063266083,0.00198519729011154,0.0420613675842382,0.036308213595461,3726,tags=34%, list=18%, signal=28%,7084/2952/1571/4830/10/4353/2944/6240/7172/654364/3704/1806/51727/6241/83549/9/1576/7371/3614/9446/119391