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23
votes
8
replies
10k
views
12 follow
what are the best resource to learn Linux bash scripting for Bioinformatics
linux shell-script
updated 16 months ago by 43k • written 9.9 years ago by ▴ 960
8
votes
5
replies
5.4k
views
6 follow
How to find GO file and do GO enrichment analysis ?
RNA-Seq genome R
updated 16 months ago by 43k • written 9.2 years ago by ▴ 960
26
votes
13
replies
42k
views
7 follow
what is the difference between GRCh37 and hg19 ?
RNA-Seq Assembly genome alignment
updated 2.1 years ago by 43k • written 9.4 years ago by ▴ 960
1
vote
1
reply
2.1k
views
comprehensive assessment of isoform quantification accuracy from RNASeq data: How much it can be wrong?
Assembly genome next-gen genomics RNA-Seq
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 960
0
votes
0
replies
13k
views
Comment: C: What is the best programming language for NGS data analysis pipeline development
updated 4.3 years ago by 43k • written 9.9 years ago by ▴ 960
0
votes
1
reply
5.2k
views
Comment: C: Which kind of microRNAs expression are measured in TCGA?
updated 4.3 years ago by 43k • written 9.9 years ago by ▴ 960
0
votes
1
reply
2.7k
views
Comment: C: Is the expression value of miRNA precursore is equivalent to it's corresponding
updated 4.3 years ago by 43k • written 10.0 years ago by ▴ 960
0
votes
0
replies
2.7k
views
Comment: C: Is the expression value of miRNA precursore is equivalent to it's corresponding
updated 4.3 years ago by 43k • written 10.0 years ago by ▴ 960
0
votes
1
reply
2.7k
views
Comment: C: Is the expression value of miRNA precursore is equivalent to it's corresponding
updated 4.3 years ago by 43k • written 10.0 years ago by ▴ 960
0
votes
1
reply
2.7k
views
Comment: C: Is the expression value of miRNA precursore is equivalent to it's corresponding
updated 4.3 years ago by 43k • written 10.0 years ago by ▴ 960
0
votes
1
reply
4.0k
views
Comment: Comment: Statistical tests for sanity check of expression data before inferring network
updated 2.6 years ago by 43k • written 10.0 years ago by ▴ 960
0
votes
0
replies
632
views
How to compute differential genome wide enrichment of specific histone marks from chip-seq data
ChIP-Seq
4.4 years ago by jack ▴ 960
0
votes
0
replies
745
views
How to intersect GWAS data with GTF or any other genomics annotation file?
genome gwas genetics SNP
updated 4.5 years ago by 20 • written 4.5 years ago by ▴ 960
6
votes
3
replies
8.3k
views
How to download reference transcriptome file of species ?
genome RNA-Seq Assembly
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 960
0
votes
1
reply
7.2k
views
Comment: C: What is the best way to quantile normalize expression matrix ?
updated 4.7 years ago by 43k • written 9.9 years ago by ▴ 960
4
votes
2
replies
2.7k
views
What does *.* represent after Ensembl transcript name ?
genome transcript Ensembl gene
updated 11 months ago by 43k • written 7.0 years ago by ▴ 960
18
votes
23
replies
7.7k
views
7 follow
How to exclude some of breast cancer subtypes just by looking at gene expression?
RNA-Seq genome cancer gene
updated 10 months ago by • 0 • written 6.4 years ago by ▴ 960
0
votes
3
replies
1.2k
views
How is it possible that multiple proteins maps to single transcript ids ?
protein RNA-Seq sequencing ChIP-Seq
updated 11 months ago by 43k • written 6.4 years ago by ▴ 960
0
votes
0
replies
2.2k
views
Comment: C: How to extract known pathways from protein protein interaction network?
6.4 years ago by jack ▴ 960
1
vote
3
replies
2.2k
views
How to extract known pathways from protein protein interaction network?
protein network pathway
6.4 years ago by jack ▴ 960
5
votes
5
replies
5.2k
views
Which kind of microRNAs expression are measured in TCGA?
next-gen RNA-Seq genome tcga
updated 13 months ago by 43k • written 9.9 years ago by ▴ 960
5
votes
4
replies
7.2k
views
What is the best way to quantile normalize expression matrix ?
RNA-Seq R software-error
updated 2.5 years ago by 43k • written 9.9 years ago by ▴ 960
2
votes
6
replies
8.5k
views
6 follow
Which version of UCSC annotation are used in TCGA RNASeqV2 isoforms expression data ?
next-gen genome RNA-Seq annotation Assembly
updated 2.0 years ago by 43k • written 9.9 years ago by ▴ 960
3
votes
5
replies
9.8k
views
Computing TPM from normalized read count from DESEQ
RNA-Seq DEseq genomics miRNA Expression
updated 6.7 years ago by 12k • written 6.7 years ago by ▴ 960
2
votes
4
replies
2.4k
views
Looking for small RNA-seq in single cell
RNA-Seq genome sequencing
updated 6.7 years ago by 7.5k • written 6.7 years ago by ▴ 960
2
votes
1
reply
1.8k
views
How to do GO enrichment alanysis at isoform levels ?
genome RNA-Seq ontology network
updated 11 months ago by 43k • written 6.7 years ago by ▴ 960
0
votes
1
reply
1.5k
views
How to map protein isoform IDs to transcripts IDs ?
RNA-Seq proteomics genome
updated 6.8 years ago by 27k • written 6.8 years ago by ▴ 960
2
votes
1
reply
1.9k
views
Is they any R package to download processed miRNA expression levle from TCGA?
next-gen RNA-Seq tca
updated 11 months ago by 43k • written 7.0 years ago by ▴ 960
2
votes
4
replies
5.5k
views
How to create your own association file for gene ontology enrichment analysis ?
enrichment ontology R software-error RNA-Seq
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 960
3
votes
8
replies
3.0k
views
7 follow
Non coding RNA expression data
gene-expression RNA-Seq
updated 15 months ago by 43k • written 9.0 years ago by ▴ 960
9
votes
13
replies
3.5k
views
What's the number at the begining of some lines of transcriptome GTF file means ?
genome-sequencing RNA-Seq Assembly genomics
updated 2.3 years ago by 43k • written 9.5 years ago by ▴ 960
0
votes
0
replies
12k
views
Comment: C: Transcript-Level Versus Gene-Level Go Enrichment Analysis (For Non-Model Organis
7.7 years ago by jack ▴ 960
21
votes
11
replies
14k
views
How to plot the heatmap of gene expression for very large data set ?
next-gen RNA-Seq R
updated 13 months ago by 43k • written 9.8 years ago by ▴ 960
1
vote
1
reply
1.6k
views
How to convert relative coordinate to aboulate coordinate at genome?
RNA-Seq genome next-gen R alignment
8.0 years ago by jack ▴ 960
2
votes
8
replies
5.9k
views
How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
RNA-Seq Assembly genomics Ensembl USCS
updated 8.0 years ago by 23k • written 8.0 years ago by ▴ 960
0
votes
1
reply
5.9k
views
Comment: C: How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
8.0 years ago by jack ▴ 960
0
votes
1
reply
5.9k
views
Comment: C: How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
8.0 years ago by jack ▴ 960
10
votes
10
replies
4.1k
views
What is best tool to call diferentially expressed isforms ?
RNA-Seq genomics R gene
updated 8.0 years ago by 7.5k • written 8.0 years ago by ▴ 960
1
vote
1
reply
1.9k
views
How to get annotation of miRNAs expression from ICGC ?
RNA-Seq mirna icgc
updated 8.0 years ago by 20 • written 8.1 years ago by ▴ 960
1
vote
1
reply
1.6k
views
non coding RNA derived from 3'-UTR
RNA-Seq RNA
updated 12 months ago by 43k • written 8.1 years ago by ▴ 960
2
votes
5
replies
1.7k
views
How to compare different annotation of transcriptome with each other?
RNA-Seq genomics
updated 12 months ago by 43k • written 8.1 years ago by ▴ 960
0
votes
1
reply
1.7k
views
Comment: C: How to compare different annotation of trasnscriptome with each other?
8.1 years ago by jack ▴ 960
0
votes
0
replies
2.0k
views
Comment: C: How to quantify noise level of estimated isoform expression levels from RNA-seq
8.1 years ago by jack ▴ 960
2
votes
2
replies
2.0k
views
How to quantify noise level of estimated isoform expression levels from RNA-seq data ?
RNA-Seq genomics
updated 12 months ago by 43k • written 8.2 years ago by ▴ 960
32
votes
8
replies
6.0k
views
How to write effective and stable bioinformatics pipeline in R ?
RNA-Seq pipeline software-error R
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 960
2
votes
3
replies
4.0k
views
How to map miRNA to transcripts of targeting genes ?
next-gen R RNA-Seq mirna
updated 2.3 years ago by 43k • written 9.7 years ago by ▴ 960
1
vote
2
replies
2.9k
views
Why FPKM value of gene expression profiles are very close to zero?
next-gen RNA-Seq
updated 13 months ago by 43k • written 8.6 years ago by ▴ 960
17
votes
4
replies
10k
views
How to get promoter coordinates of hg19 from UCSC genome browser ?
gene Assembly genomics
updated 19 months ago by 43k • written 8.6 years ago by ▴ 960
0
votes
1
reply
2.0k
views
What is the best human 3'-UTR annotation?
RNA-Seq sequence genomics
updated 19 months ago by 43k • written 8.7 years ago by ▴ 960
0
votes
1
reply
2.4k
views
What are the good tools for mRNA codon usage optimization and secondary structure prediction?
genomics
updated 18 months ago by 43k • written 8.7 years ago by ▴ 960
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