# HG changeset patch # User mvdbeek # Date 1457179506 18000 # Node ID a903407e3ca0a8fb82bced89fecdf75cd50cfc99 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty diff -r 000000000000 -r a903407e3ca0 deseq2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq2.xml Sat Mar 05 07:05:06 2016 -0500 @@ -0,0 +1,56 @@ + diff -r 000000000000 -r a903407e3ca0 test-data/counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counts.tab Sat Mar 05 07:05:06 2016 -0500 @@ -0,0 +1,500 @@ +Geneid 2: Oocyte 1: accepted_hits 3: Oocyte 2: accepted_hits 4: Pronuclei 1: accepted_hits 5: pronuclei 2: accepted_hits 6: Pronuclei 3: accepted_hits +NM_001195025 0 0 0 0 0 +NM_028778 0 0 0 0 0 +NM_001290393 0 0 0 0 0 +NM_008922 3133 2276 2288 2659 820 +NM_175370 4 22 7 16 9 +NM_001290390 0 0 0 0 0 +NM_175642 977 1711 1013 459 430 +NM_001290392 0 0 0 0 0 +NM_027671 0 0 0 0 0 +NM_178884 0 0 0 2 3 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6.17530543030933 0.862182867065928 0.729016942588022 1.18266506126067 0.236941916299098 NA +NM_146112 0 0 0 NA NA NA NA NA +NM_010566 0 0 0 NA NA NA NA NA +NR_122078 0 0 0 NA NA NA NA NA +NM_201642 0 0 0 NA NA NA NA NA +NM_201641 0 0 0 NA NA NA NA NA +NM_001110193 0 0 0 NA NA NA NA NA +NM_145079 0 0 0 NA NA NA NA NA +NM_029269 0 0 0 NA NA NA NA NA +NM_139152 0 0 0 NA NA NA NA NA +NM_178119 0.942207696785575 3.45816490398115 2.45178202110292 0.23912879124041 0.590086443595563 0.405243661900333 0.685298413793502 NA +NM_001037136 0 0 0 NA NA NA NA NA +NM_001111312 0 0.369943959061015 0.221966375436609 0.251236829594032 0.484659763413011 0.518377733329465 0.604194747223895 NA +NM_001243009 0 0 0 NA NA NA NA NA +NM_001243008 0 0 0 NA NA NA NA NA +NM_023046 0 0 0 NA NA NA NA NA +NM_001039126 0 0 0 NA NA NA NA NA +NM_007855 0 0 0 NA NA NA NA NA +NM_001271884 0 0 0 NA NA NA NA NA +NM_207031 0 1.04774465237167 0.628646791423002 0.31923308341291 0.532154371221071 0.59988811645088 0.548580802705268 NA +NM_172463 37.6605416637659 8.27272545553742 20.0278519388288 -1.36450538728293 0.80057392783942 -1.70440897440346 0.0883047084715896 NA +NM_008798 6.76962693881753 22.490873287303 16.2023747479088 0.612702946002264 0.802129735826712 0.763845196900454 0.444959499193142 NA +NR_040467 0 0 0 NA NA NA NA NA +NM_028942 0 0 0 NA NA NA NA NA +NR_120500 13.0879454150472 25.7366540925439 20.6771706215453 0.397553100481943 0.814316545181192 0.488204621205976 0.625404911601836 NA +NM_027584 0 0 0 NA NA NA NA NA +NM_001164233 0 0 0 NA NA NA NA NA +NM_013626 4.16075309231528 5.46445760829258 4.94297580190166 0.11114846061368 0.742510223014856 0.14969283542303 0.881006960992266 NA +NM_173187 0 0 0 NA NA NA NA NA +NM_009399 0 1.47977583624406 0.887865501746437 0.333753920102786 0.540973444950313 0.61695065297233 0.537267275055595 NA +NM_178779 0 0 0 NA NA NA NA NA +NM_029349 0 0 0 NA NA NA NA NA +NM_001160368 0 0 0 NA NA NA NA NA +NM_009741 14.4814615744206 14.9625266561117 14.7701006234353 0.0250257143887851 0.824676761721047 0.0303460889774049 0.975791039793048 NA +NM_198028 0 0 0 NA NA NA NA NA +NM_001160307 0 0 0 NA NA NA NA NA +NR_102307 0 0 0 NA NA NA NA NA +NR_102306 0 0 0 NA NA NA NA NA +NM_172853 0 8.7031681175022 5.22190087050132 0.563197806076453 0.647878985885826 0.869294757733821 NA NA +NM_001077425 0 14.6886569031533 8.81319414189195 1.13270305596256 0.771815467334734 1.46758273693848 0.14221760004542 NA +NM_029709 0 0 0 NA NA NA NA NA +NM_001293300 0 0.280747358629103 0.168448415177462 0.236266271681685 0.47261510198017 0.499912657661113 0.617136579212974 NA +NM_001293301 0 0 0 NA NA NA NA NA +NM_022327 0 0 0 NA NA NA NA NA +NM_001172074 2.31592847035403 1.87682917092561 2.05246889069698 -0.0512918580082018 0.609262188750539 -0.0841868393530049 0.932907881715578 NA +NM_133186 0 0 0 NA NA NA NA NA +NM_001085409 0 0 0 NA NA NA NA NA +NM_028439 0 0 0 NA NA NA NA NA +NM_178082 0 0 0 NA NA NA NA NA +NM_029955 0 0 0 NA NA NA NA NA +NM_133748 0 0 0 NA NA NA NA NA +NM_001271532 0 0 0 NA NA NA NA NA +NM_001271531 0 0 0 NA NA NA NA NA +NM_001025156 0 0 0 NA NA NA NA NA +NM_027677 1.80523385035134 2.58960771342711 2.2758581681968 0.0651401260613425 0.556538034797777 0.117045236782445 0.906824206046482 NA +NM_145100 0 0 0 NA NA NA NA NA +NM_001033041 0 0 0 NA NA NA NA NA +NM_001285945 0 0 0 NA NA NA NA NA +NM_145128 0.902616925175671 24.3191660046423 14.9525463728557 1.95361459558199 0.824630542310642 2.36907863018012 0.017832461848317 NA +NM_027678 0 0.369943959061015 0.221966375436609 0.251236829594032 0.484659763413011 0.518377733329465 0.604194747223895 NA +NM_172485 281.810844108409 273.901284979979 277.065108631351 -0.0344125191892855 0.516914896097389 -0.0665728913000837 NA NA +NM_026976 0 0 0 NA NA NA NA NA +NM_007799 0 0 0 NA NA NA NA NA +NM_172510 8.00876542267739 20.284760304162 15.3743623515682 0.611900915963187 0.823917669299397 0.742672403765179 0.457680041250665 NA +NM_175294 0 0 0 NA NA NA NA NA +NM_001145804 0 0 0 NA NA NA NA NA +NM_001160318 0 0 0 NA NA NA NA NA +NM_001160317 0 0 0 NA NA NA NA NA +NM_001160316 0 0 0 NA NA NA NA NA +NM_182716 0 1.53399458748513 0.920396752491081 0.334952026879345 0.541682645308212 0.618354731835207 0.536341530882536 NA +NM_144530 0 0 0 NA NA NA NA NA +NM_001276767 0 0 0 NA NA NA NA NA +NM_001145300 0 0 0 NA NA NA NA NA +NM_053106 0 0 0 NA NA NA NA NA +NM_001291015 0 0 0 NA NA NA NA NA +NM_177642 0 0.766997293742567 0.46019837624554 0.301930674074754 0.521081592818901 0.579430703820099 0.562298591673325 NA +NM_030676 0 0 0 NA NA NA NA NA +NM_001159769 0 0.383498646871284 0.23009918812277 0.253165513151483 0.486165361864932 0.520739511717451 0.602548245637964 NA +NM_011210 0 0 0 NA NA NA NA NA +NM_001111316 0 0 0 NA NA NA NA NA +NM_001268286 0 0 0 NA NA NA NA NA +NM_181347 0 0 0 NA NA NA NA NA +NM_001166501 0.451308462587835 1.13694125280358 0.862688136717284 0.14483340196651 0.542474828609351 0.2669864007106 0.789479631817819 NA +NR_040455 0 0 0 NA NA NA NA NA 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0.236159941499862 0.655339498277251 0.360362746516388 0.71857588174249 NA +NR_108050 0 0 0 NA NA NA NA NA +NR_046171 0 0 0 NA NA NA NA NA +NM_177838 0 0 0 NA NA NA NA NA +NM_001277730 0 0 0 NA NA NA NA NA +NM_001134741 3.66985385811754 7.77979843828435 6.13582060621763 0.384559430761919 0.797430774550789 0.482248043384769 0.629629751412181 NA +NM_026683 0 0 0 NA NA NA NA NA +NM_023141 4.06177616329052 13.4806387799198 9.71309373326807 0.511865528371584 0.773248932023639 0.661967326656372 0.50799216160275 NA +NR_027640 0.471103848392788 0 0.188441539357115 -0.343626431501831 0.478911579314015 -0.717515396044581 0.473056140037951 NA +NM_001159968 0 0 0 NA NA NA NA NA +NM_001159965 0 0 0 NA NA NA NA NA +NM_001159967 0 0 0 NA NA NA NA NA +NM_001159966 0 0 0 NA NA NA NA NA +NM_023884 0 0 0 NA NA NA NA NA +NR_038031 0 0 0 NA NA NA NA NA +NR_038030 0 0 0 NA NA NA NA NA +NM_001162896 0 0 0 NA NA NA NA NA +NM_001038619 0 0 0 NA NA NA NA NA +NM_172646 0 0 0 NA NA NA NA NA +NM_001293313 0 0 0 NA NA NA NA NA +NM_138314 0 0 0 NA NA NA NA NA +NM_001081126 0.942207696785575 0.766997293742567 0.83708145495977 -0.0390258061465042 0.54270349190546 -0.0719099963950527 0.942673534674585 NA +NM_001164306 6.31831847622969 6.05345883164822 6.15940268948081 -0.0158292992457534 0.727327354869798 -0.0217636517309144 0.982636489031444 NA +NM_001160049 0 0 0 NA NA NA NA NA +NM_001033344 0 0 0 NA NA NA NA NA +NM_198932 0 0 0 NA NA NA NA NA +NM_011137 0 0 0 NA NA NA NA NA +NM_030724 42.7278970921829 746.296046918467 464.868786987954 3.76305551214874 0.461005878034587 8.16270614203842 NA NA +NM_033652 7.33970771623508 41.9683654481833 28.116902355404 1.66404402883696 0.768767950863607 2.16455957479449 0.0304214296407256 NA +NM_175461 0 0 0 NA NA NA NA NA +NM_001160261 0 0 0 NA NA NA NA NA +NM_001160262 0 0 0 NA NA NA NA NA +NM_183355 0 0 0 NA NA NA NA NA +NM_008783 0 0 0 NA NA NA NA NA +NM_001291509 0 0 0 NA NA NA NA NA +NM_001291508 0 0 0 NA NA NA NA NA +NM_027528 0.942207696785575 0 0.37688307871423 -0.420087470788302 0.514998495489618 -0.815706209760705 0.414668186551214 NA +NM_013489 0 0 0 NA NA NA NA NA diff -r 000000000000 -r a903407e3ca0 test-data/dge.tab.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dge.tab.re_match Sat Mar 05 07:05:06 2016 -0500 @@ -0,0 +1,500 @@ +gene\ baseMeanA\ baseMeanB\ baseMean\ log2FoldChange\ lfcSE\ stat\ pvalue\ padj +NM\_001290814\ 13\.8361846647093\ 302\.692276889662\ 187\.149839999681\ 4\.02298530293272\ 0\.475300264296235\ 8\.46409229098463\ 2\.58155340319795e\-17\ 3\.84651457076494e\-15 +NM\_175296\ 42\.3873901225727\ 938\.523758683365\ 580\.069211259048\ 3\.98548352659215\ 0\.502124973720984\ 7\.93723422489391\ 2\.06739417563206e\-15\ 1\.54020866084588e\-13 +NM\_010472\ 166\.814206844757\ 1470\.37801982385\ 948\.952494632214\ 2\.93850691094032\ 0\.401906370179809\ 7\.31142158713647\ 2\.643307621836e\-13\ 1\.31284278551188e\-11 +NM\_029342\ 102\.585720376899\ 642\.349793886348\ 426\.444164482568\ 2\.47979721531494\ 0\.398185092542637\ 6\.22775001314096\ 4\.73181277129915e\-10\ 1\.76260025730893e\-08 +NM\_001033408\ 10\.067353877567\ 192\.663868743505\ 119\.62526279713\ 3\.55941286675189\ 0\.592903302264483\ 6\.0033615146979\ 1\.93273620816604e\-09\ 5\.75955390033481e\-08 +NM\_008801\ 238\.766220843347\ 1165\.70420032215\ 794\.929008530628\ 2\.16023652550394\ 0\.376164519001384\ 5\.74279714428886\ 9\.31252640346199e\-09\ 2\.31261072352639e\-07 +NM\_199021\ 342\.796872715182\ 1102\.82797928137\ 798\.815536654893\ 1\.6260740249254\ 0\.304536884403641\ 5\.33949780207956\ 9\.32043996944546e\-08\ 1\.98392222206768e\-06 +NM\_009255\ 27214\.4775715473\ 10819\.482196131\ 17377\.4803462975\ \-1\.29469303336041\ 0\.268165046272498\ \-4\.82797087598358\ 1\.3793125924685e\-06\ 2\.56896970347259e\-05 +NM\_023645\ 2043\.5349277896\ 759\.207151422419\ 1272\.93826196929\ \-1\.38274254401162\ 0\.289726371358106\ \-4\.77258089255026\ 1\.81880019099805e\-06\ 2\.89691190975949e\-05 +NM\_172849\ 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1\.69474947951718\ 0\.499191266553957\ 3\.39499024335193\ 0\.0006863104627267\ 0\.00464819358846719 +NM\_009581\ 9\.18453233819633\ 79\.6145738440232\ 51\.4425572416925\ 2\.35539055140344\ 0\.692796709020918\ 3\.39982930163186\ 0\.000674279329052518\ 0\.00464819358846719 +NM\_025819\ 7436\.56591598075\ 4157\.76659247737\ 5469\.28632187872\ \-0\.820136402488323\ 0\.243431843899217\ \-3\.3690596486952\ 0\.000754251042909209\ 0\.00488623501710748 +NM\_001277076\ 10\.6176392691796\ 95\.767407773599\ 61\.7075003718312\ 2\.33678175827228\ 0\.710230094690954\ 3\.29017564271068\ 0\.00100124862426847\ 0\.00621608520900009 +NM\_026719\ 949\.926448892427\ 455\.046155963654\ 652\.998273135163\ \-1\.02094827570642\ 0\.318111375253008\ \-3\.2094051176083\ 0\.00133009938283553\ 0\.00792739232169974 +NM\_133239\ 146\.730914425186\ 396\.719385405167\ 296\.723997013175\ 1\.33565408433631\ 0\.418546380184067\ 3\.19117342204447\ 0\.00141696200430467\ 0\.00812028225543832 +NM\_028250\ 4\.22013924973014\ 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-0,0 +1,9 @@ + + + + + + + + +