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23
votes
8
replies
9.4k
views
12 follow
what are the best resource to learn Linux bash scripting for Bioinformatics
linux shell-script
updated 3 months ago by 38k • written 8.9 years ago by ▴ 960
8
votes
5
replies
4.9k
views
6 follow
How to find GO file and do GO enrichment analysis ?
RNA-Seq genome R
updated 3 months ago by 38k • written 8.2 years ago by ▴ 960
26
votes
13
replies
38k
views
7 follow
what is the difference between GRCh37 and hg19 ?
RNA-Seq Assembly genome alignment
updated 12 months ago by 38k • written 8.3 years ago by ▴ 960
1
vote
1
reply
2.0k
views
comprehensive assessment of isoform quantification accuracy from RNASeq data: How much it can be wrong?
Assembly genome next-gen genomics RNA-Seq
updated 11 months ago by 38k • written 8.1 years ago by ▴ 960
0
votes
0
replies
11k
views
Comment: C: What is the best programming language for NGS data analysis pipeline development
updated 3.2 years ago by 38k • written 8.9 years ago by ▴ 960
0
votes
1
reply
4.8k
views
Comment: C: Which kind of microRNAs expression are measured in TCGA?
updated 3.2 years ago by 38k • written 8.9 years ago by ▴ 960
0
votes
1
reply
2.1k
views
Comment: C: Is the expression value of miRNA precursore is equivalent to it's corresponding
updated 3.2 years ago by 38k • written 8.9 years ago by ▴ 960
0
votes
0
replies
2.1k
views
Comment: C: Is the expression value of miRNA precursore is equivalent to it's corresponding
updated 3.2 years ago by 38k • written 8.9 years ago by ▴ 960
0
votes
1
reply
2.1k
views
Comment: C: Is the expression value of miRNA precursore is equivalent to it's corresponding
updated 3.2 years ago by 38k • written 8.9 years ago by ▴ 960
0
votes
1
reply
2.1k
views
Comment: C: Is the expression value of miRNA precursore is equivalent to it's corresponding
updated 3.2 years ago by 38k • written 8.9 years ago by ▴ 960
0
votes
1
reply
3.5k
views
Comment: Comment: Statistical tests for sanity check of expression data before inferring network
updated 18 months ago by 38k • written 8.9 years ago by ▴ 960
0
votes
0
replies
529
views
How to compute differential genome wide enrichment of specific histone marks from chip-seq data
ChIP-Seq
3.3 years ago by jack ▴ 960
0
votes
0
replies
598
views
How to intersect GWAS data with GTF or any other genomics annotation file?
genome gwas genetics SNP
updated 3.5 years ago by 20 • written 3.5 years ago by ▴ 960
6
votes
3
replies
7.1k
views
How to download reference transcriptome file of species ?
genome RNA-Seq Assembly
updated 15 months ago by 38k • written 8.7 years ago by ▴ 960
0
votes
1
reply
6.7k
views
Comment: C: What is the best way to quantile normalize expression matrix ?
updated 3.7 years ago by 38k • written 8.8 years ago by ▴ 960
4
votes
2
replies
2.3k
views
What does *.* represent after Ensembl transcript name ?
bioinformatics gene transcript genome Ensembl
updated 4.5 years ago by 11k • written 5.9 years ago by ▴ 960
18
votes
22
replies
5.9k
views
6 follow
How to exclude some of breast cancer subtypes just by looking at gene expression?
RNA-Seq genome cancer gene
updated 22 months ago by ▴ 40 • written 5.3 years ago by ▴ 960
0
votes
3
replies
961
views
How is it possible that multiple proteins maps to single transcript ids ?
RNA-Seq ChIP-Seq sequencing protein bioinformatics
updated 5.3 years ago by 97k • written 5.3 years ago by ▴ 960
0
votes
0
replies
1.9k
views
Comment: C: How to extract known pathways from protein protein interaction network?
5.4 years ago by jack ▴ 960
1
vote
3
replies
1.9k
views
How to extract known pathways from protein protein interaction network?
protein network pathway
5.4 years ago by jack ▴ 960
5
votes
5
replies
4.8k
views
Which kind of microRNAs expression are measured in TCGA?
next-gen RNA-Seq genome tcga
updated 8 days ago by 38k • written 8.9 years ago by ▴ 960
5
votes
4
replies
6.7k
views
What is the best way to quantile normalize expression matrix ?
RNA-Seq R software-error
updated 17 months ago by 38k • written 8.8 years ago by ▴ 960
2
votes
6
replies
8.1k
views
6 follow
Which version of UCSC annotation are used in TCGA RNASeqV2 isoforms expression data ?
next-gen genome RNA-Seq annotation Assembly
updated 11 months ago by 38k • written 8.8 years ago by ▴ 960
3
votes
5
replies
8.8k
views
Computing TPM from normalized read count from DESEQ
RNA-Seq DEseq genomics miRNA Expression
updated 5.6 years ago by 12k • written 5.6 years ago by ▴ 960
2
votes
4
replies
2.1k
views
Looking for small RNA-seq in single cell
RNA-Seq genome sequencing
updated 5.6 years ago by 7.4k • written 5.6 years ago by ▴ 960
2
votes
1
reply
1.5k
views
How to do GO enrichment alanysis at isoform levels ?
RNA-Seq bioinformatics genome network ontology
updated 5.7 years ago by 7.4k • written 5.7 years ago by ▴ 960
0
votes
1
reply
1.3k
views
How to map protein isoform IDs to transcripts IDs ?
RNA-Seq proteomics genome
updated 5.7 years ago by 26k • written 5.7 years ago by ▴ 960
2
votes
1
reply
1.7k
views
Is they any R package to download processed miRNA expression levle from TCGA?
RNA-Seq next-gen tca bioinformatics
updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by ▴ 960
2
votes
4
replies
5.0k
views
How to create your own association file for gene ontology enrichment analysis ?
enrichment ontology R software-error RNA-Seq
updated 11 months ago by 38k • written 8.2 years ago by ▴ 960
3
votes
8
replies
2.6k
views
7 follow
Non coding RNA expression data
gene-expression RNA-Seq
updated 9 weeks ago by 38k • written 7.9 years ago by ▴ 960
9
votes
13
replies
3.0k
views
What's the number at the begining of some lines of transcriptome GTF file means ?
genome-sequencing RNA-Seq Assembly genomics
updated 14 months ago by 38k • written 8.5 years ago by ▴ 960
0
votes
0
replies
11k
views
Comment: C: Transcript-Level Versus Gene-Level Go Enrichment Analysis (For Non-Model Organis
6.6 years ago by jack ▴ 960
21
votes
11
replies
12k
views
How to plot the heatmap of gene expression for very large data set ?
next-gen RNA-Seq R
updated 23 days ago by 38k • written 8.8 years ago by ▴ 960
1
vote
1
reply
1.4k
views
How to convert relative coordinate to aboulate coordinate at genome?
RNA-Seq genome next-gen R alignment
6.9 years ago by jack ▴ 960
2
votes
8
replies
5.2k
views
How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
RNA-Seq Assembly genomics Ensembl USCS
updated 6.9 years ago by 23k • written 6.9 years ago by ▴ 960
0
votes
1
reply
5.2k
views
Comment: C: How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
6.9 years ago by jack ▴ 960
0
votes
1
reply
5.2k
views
Comment: C: How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
6.9 years ago by jack ▴ 960
10
votes
10
replies
3.5k
views
What is best tool to call diferentially expressed isforms ?
RNA-Seq genomics R gene
updated 6.9 years ago by 7.4k • written 6.9 years ago by ▴ 960
1
vote
1
reply
1.8k
views
How to get annotation of miRNAs expression from ICGC ?
RNA-Seq mirna icgc
updated 6.9 years ago by 20 • written 7.0 years ago by ▴ 960
1
vote
1
reply
1.5k
views
non coding RNA derived from 3'-UTR
RNA-Seq RNA Bioinformatics
updated 7.0 years ago by 52k • written 7.0 years ago by ▴ 960
2
votes
5
replies
1.4k
views
How to compare different annotation of trasnscriptome with each other?
genomics RNA-Seq Bioinformatics
updated 7.0 years ago by ★ 2.1k • written 7.0 years ago by ▴ 960
0
votes
1
reply
1.4k
views
Comment: C: How to compare different annotation of trasnscriptome with each other?
7.0 years ago by jack ▴ 960
0
votes
0
replies
1.8k
views
Comment: C: How to quantify noise level of estimated isoform expression levels from RNA-seq
7.1 years ago by jack ▴ 960
2
votes
2
replies
1.8k
views
How to quantify noise level of estimated isoform expression levels from RNA-seq data ?
RNA-Seq bioinformatics genomics
7.1 years ago by jack ▴ 960
32
votes
8
replies
5.3k
views
How to write effective and stable bioinformatics pipeline in R ?
RNA-Seq pipeline software-error R
updated 14 months ago by 38k • written 8.5 years ago by ▴ 960
2
votes
3
replies
3.8k
views
How to map miRNA to transcripts of targeting genes ?
next-gen R RNA-Seq mirna
updated 14 months ago by 38k • written 8.6 years ago by ▴ 960
1
vote
2
replies
2.6k
views
Why FPKM value of gene expression profiles are very close to zero?
RNA-Seq bioinformatics next-gen
updated 6 months ago by 38k • written 7.5 years ago by ▴ 960
17
votes
4
replies
9.2k
views
How to get promoter coordinates of hg19 from UCSC genome browser ?
gene Assembly genomics
updated 6 months ago by 38k • written 7.5 years ago by ▴ 960
0
votes
1
reply
1.8k
views
What is the best human 3'-UTR annotation?
RNA-Seq sequence genomics
updated 6 months ago by 38k • written 7.6 years ago by ▴ 960
0
votes
1
reply
2.2k
views
What are the good tools for mRNA codon usage optimization and secondary structure prediction?
genomics
updated 5 months ago by 38k • written 7.6 years ago by ▴ 960
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