add kallisto to list of tools

Author: malachig

manuscript/supplementary_tables/supplementary_table_2_urls.md

@@ -12,7 +12,7 @@ All tools used in the online tutorial (www.rnaseq.wiki) are referenced below (in
 | **Small RNA identification and characterization (e.g., miRNAs)** [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25319663">25319663</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/23720668">23720668</a>] | ShortStack [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23610128">23610128</a>], CoRAL [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24145223">24145223</a>], MTide [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25256573">25256573</a>], FlaiMapper [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25338717">25338717</a>], miRPlant [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25117656">25117656</a>], PROmiRNA [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23958307">23958307</a>], omiRas [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23946503">23946503</a>], DREAM [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25840043">25840043</a>]. |
 | **Transcript assembly (reference genome guided)** [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24185837">24185837</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/21897427">21897427</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/23393030">23393030</a>] | Cufflinks [<a href="http://www.ncbi.nlm.nih.gov/pubmed/20436464">20436464</a>], Scripture [<a href="http://www.ncbi.nlm.nih.gov/pubmed/20436462">20436462</a>], StringTie [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25690850">25690850</a>], bayesembler [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25367074">25367074</a>], IsoLasso [<a href="http://www.ncbi.nlm.nih.gov/pubmed/21951053">21951053</a>]. |
 | **Transcript assembly (de novo, reference genome free)** [<a href="http://www.ncbi.nlm.nih.gov/pubmed/21897427">21897427</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/23393030">23393030</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/23056003">23056003</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/23666209">23666209</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/25084827">25084827</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/25279728">25279728</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/25788326">25788326</a>] | Trinity [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23845962">23845962</a>], Trans-ABySS [<a href="http://www.ncbi.nlm.nih.gov/pubmed/20935650">20935650</a>], Oases [<a href="http://www.ncbi.nlm.nih.gov/pubmed/22368243">22368243</a>], RSEM [<a href="http://www.ncbi.nlm.nih.gov/pubmed/21816040">21816040</a>], DETONATE [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25608678">25608678</a>], SEECER (sequencing error correction for assembly) [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23558750">23558750</a>], BRANCH [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23493323">23493323</a>] uses partial or related genomics sequences as a guide, EBARDenovo [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23457040">23457040</a>], Bridger [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25723335">25723335</a>]. |
-| **Transcript abundance or expression estimation (FPKM/RPKM)** [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24185837">24185837</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24885830">24885830</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24109770">24109770</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24685233">24685233</a>] | Cufflinks [<a href="http://www.ncbi.nlm.nih.gov/pubmed/20436464">20436464</a>], eXpress [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23160280">23160280</a>], RSEM [<a href="http://www.ncbi.nlm.nih.gov/pubmed/21816040">21816040</a>], Sailfish (alignment free) [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24752080">24752080</a>], RNA-Skim (alignment free) [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24931995">24931995</a>], MITIE [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23980025">23980025</a>], ireckon [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23204306">23204306</a>], DRUT [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23202426">23202426</a>]. |
+| **Transcript abundance or expression estimation (FPKM/RPKM)** [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24185837">24185837</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24885830">24885830</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24109770">24109770</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24685233">24685233</a>] | Cufflinks [<a href="http://www.ncbi.nlm.nih.gov/pubmed/20436464">20436464</a>], eXpress [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23160280">23160280</a>], RSEM [<a href="http://www.ncbi.nlm.nih.gov/pubmed/21816040">21816040</a>], Sailfish (alignment free) [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24752080">24752080</a>], RNA-Skim (alignment free) [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24931995">24931995</a>], MITIE [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23980025">23980025</a>], ireckon [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23204306">23204306</a>], DRUT [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23202426">23202426</a>], Kallisto (alignment free) [<a href="http://arxiv.org/abs/1505.02710">arXiv</a>]. |
 | **Obtaining raw transcript/gene read counts (FPM/RPM)** [<a href="http://www.ncbi.nlm.nih.gov/pubmed/21176179">21176179</a>] | HTSeq [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25260700">25260700</a>], FeatureCounts [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24227677">24227677</a>], Rcount [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25322836">25322836</a>], maxcounts [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24564404">24564404</a>], FIXSEQ (adjusts counts to compensate for overdispersion) [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24603409">24603409</a>], Cuffquant. |
 | **Differential expression** [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25119138">25119138</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24300110">24300110</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24020486">24020486</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/25024085">25024085</a>] | Cuffdiff [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23222703">23222703</a>], limma [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25605792">25605792</a>], DESeq2 [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25516281">25516281</a>], EdgeR [<a href="http://www.ncbi.nlm.nih.gov/pubmed/19910308">19910308</a>], Corset (for de novo assembled transcriptomes) [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25063469">25063469</a>], sSeq [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23589650">23589650</a>], BADGE [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25252852">25252852</a>], compcodeR [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24813215">24813215</a>], metaRNASeq [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24678608">24678608</a>], Characteristic Direction [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24650281">24650281</a>], NPEBseq [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23981227">23981227</a>]. |
 | **Alternative splicing, alternative expression** [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24447644">24447644</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24885830">24885830</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24058384">24058384</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24549677">24549677</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/24951248">24951248</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/25511303">25511303</a>] | Cuffdiff [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23222703">23222703</a>], DEXSeq [<a href="http://www.ncbi.nlm.nih.gov/pubmed/22722343">22722343</a>], ALEXA-seq [<a href="http://www.ncbi.nlm.nih.gov/pubmed/20835245">20835245</a>], IUTA [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25283306">25283306</a>], FineSplice [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24574529">24574529</a>], PennSeq [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24362841">24362841</a>], FlipFlop [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24813214">24813214</a>], SNPlice [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25481010">25481010</a>], spliceR [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24655717">24655717</a>], GESS [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24447644">24447644</a>], RNASeq-MATS [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23872975">23872975</a>], SplicingCompass [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23449093">23449093</a>], DiffSplice [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23155066">23155066</a>], SigFuge [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25030904">25030904</a>], SUPPA [bioRXiv], CLASS [bioRXiv], SplAdder [bioRXiv], SplicePie [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25800735">25800735</a>]. |