User: archie

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archie40
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India
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3 days, 14 hours ago
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4 years, 2 months ago
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Posts by archie

<prev • 42 results • page 1 of 5 • next >
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non matched control for PDAC samples
... Dear all, Dear all, I have RNA-Seq samples of pancreatic patients. but I do not have matched control samples. Sequencing of matched control samples was not done, due to some technical issues. But, I want to use control samples in this study. What are possible non matched control samples that could ...
pdac tcga rna-seq tumour written 19 days ago by archie40 • updated 9 days ago by Kevin Blighe19k
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Comment: C: error in downloading kissplice
... Dear Leandro Its working now . Thank you so much ...
written 20 days ago by archie40
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error in downloading kissplice
... Dear developers I have issue downloading the kissplice from website http://kissplice.prabi.fr/tools/kiss2rt/ KisSplice2RefTranscriptome version 1.3.2 I am not able to open this page. could you please resolve it. Kind regards Archana ...
kissplice written 23 days ago by archie40 • updated 22 days ago by leandro.ishi.lima70
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choice of human genome before RNASeq mapping
... Dear all, I have RNASEQ data and want to map against the reference genome. I download human genome from ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/ Toplevel sequences unmasked: Homo_sapiens.GRCh38.dna.toplevel.fa.gz Here, I found other format files such as Toplevel soft/ ...
human genome ensembl rnaseq mapping written 8 weeks ago by archie40 • updated 8 weeks ago by grant.hovhannisyan780
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Answer: A: comparison of expression profile between 2 groups
... Hello , For comparative mutation and expression data, you can use gitools available at http://www.gitools.org/home . Here, you can give input of multi dimesional data at a time and can get comprehensive results. You can find many tutorial for detail usage of this tool. ...
written 9 weeks ago by archie40
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Answer: A: Variant calling for a polyploid species
... Hello You can check SNiPloid https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791807/ This article can help you to go further in order to predict homeologus SNPs . I hope it will help you. ...
written 9 weeks ago by archie40
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genlist for clusterprofiler
... Dear all, I am using the clusterprofiler. I used the enrichGO, enrichKEGG and enrichDO . data<-read.delim("enrich.txt") genes<-data$entrez[abs(data$expr)>2] I used genes as input in enrichGO,enirchKEGG. But I am not able to create input geneList for the gse function . ego3 <- gseG ...
clusterprofiler written 10 weeks ago by archie40 • updated 10 weeks ago by Guangchuang Yu1.8k
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Comment: C: wgcna modules detection and MEs
... Dear Fereshteh I checked moduleColors table count (also named as mergedColors) which consist of total of all genes into multiple modules where gene count matches to my input list. I missed this point earlier . Thank you for your suggestion :) ...
written 10 weeks ago by archie40
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wgcna modules detection and MEs
... Dear all, Recently I have gone through tutorial of WGCNA and performed Module identification using dynamic tree cut and saved output in variable dynamicMods. Then, I proceeded for Merging of modules whose expression profiles are very similar. As a result found Eigengenes of the new merged modu ...
wgcna written 10 weeks ago by archie40
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Comment: C: From gene list to disease ontology
... Dear all, I just found this link https://bioconductor.org/packages/devel/bioc/vignettes/DOSE/inst/doc/enrichmentAnalysis.html#enrichdo-function where gene disease association could be done by using enrichDO function . May be useful for those who are working in this area. Thank you ...
written 11 weeks ago by archie40

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