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23
votes
8
replies
11k
views
12 follow
what are the best resource to learn Linux bash scripting for Bioinformatics
linux shell-script
updated 2.4 years ago by 45k • written 10.9 years ago by ▴ 990
8
votes
5
replies
6.1k
views
6 follow
How to find GO file and do GO enrichment analysis ?
RNA-Seq genome R
updated 2.3 years ago by 45k • written 10.2 years ago by ▴ 990
27
votes
13
replies
45k
views
7 follow
what is the difference between GRCh37 and hg19 ?
RNA-Seq Assembly genome alignment
updated 3.1 years ago by 45k • written 10.3 years ago by ▴ 990
1
vote
1
reply
2.3k
views
comprehensive assessment of isoform quantification accuracy from RNASeq data: How much it can be wrong?
Assembly genome next-gen genomics RNA-Seq
updated 3.0 years ago by 45k • written 10.2 years ago by ▴ 990
0
votes
0
replies
749
views
How to compute differential genome wide enrichment of specific histone marks from chip-seq data
ChIP-Seq
5.3 years ago by jack ▴ 990
0
votes
0
replies
881
views
How to intersect GWAS data with GTF or any other genomics annotation file?
genome gwas genetics SNP
updated 5.5 years ago by 20 • written 5.5 years ago by ▴ 990
6
votes
3
replies
9.2k
views
How to download reference transcriptome file of species ?
genome RNA-Seq Assembly
updated 3.4 years ago by 45k • written 10.7 years ago by ▴ 990
4
votes
2
replies
3.1k
views
What does *.* represent after Ensembl transcript name ?
genome transcript Ensembl gene
updated 23 months ago by 45k • written 8.0 years ago by ▴ 990
19
votes
23
replies
9.0k
views
7 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 • 0 • written 7.4 years ago by ▴ 990
0
votes
3
replies
1.4k
views
How is it possible that multiple proteins maps to single transcript ids ?
protein RNA-Seq sequencing ChIP-Seq
updated 23 months ago by 45k • written 7.4 years ago by ▴ 990
1
vote
3
replies
2.5k
views
How to extract known pathways from protein protein interaction network?
protein network pathway
7.4 years ago by jack ▴ 990
5
votes
5
replies
5.6k
views
Which kind of microRNAs expression are measured in TCGA?
next-gen RNA-Seq genome tcga
updated 2.1 years ago by 45k • written 10.9 years ago by ▴ 990
5
votes
4
replies
7.7k
views
What is the best way to quantile normalize expression matrix ?
RNA-Seq R software-error
updated 3.5 years ago by 45k • written 10.9 years ago by ▴ 990
2
votes
6
replies
9.0k
views
6 follow
Which version of UCSC annotation are used in TCGA RNASeqV2 isoforms expression data ?
next-gen genome RNA-Seq annotation Assembly
updated 3.0 years ago by 45k • written 10.9 years ago by ▴ 990
3
votes
5
replies
11k
views
Computing TPM from normalized read count from DESEQ
RNA-Seq DEseq genomics miRNA Expression
updated 7.7 years ago by 12k • written 7.7 years ago by ▴ 990
2
votes
4
replies
2.7k
views
Looking for small RNA-seq in single cell
RNA-Seq genome sequencing
updated 7.7 years ago by 7.6k • written 7.7 years ago by ▴ 990
2
votes
1
reply
2.0k
views
How to do GO enrichment alanysis at isoform levels ?
genome RNA-Seq ontology network
updated 23 months ago by 45k • written 7.7 years ago by ▴ 990
0
votes
1
reply
1.7k
views
How to map protein isoform IDs to transcripts IDs ?
RNA-Seq proteomics genome
updated 7.8 years ago by 27k • written 7.8 years ago by ▴ 990
2
votes
1
reply
2.1k
views
Is they any R package to download processed miRNA expression levle from TCGA?
next-gen RNA-Seq tca
updated 23 months ago by 45k • written 8.0 years ago by ▴ 990
2
votes
4
replies
6.0k
views
How to create your own association file for gene ontology enrichment analysis ?
enrichment ontology R software-error RNA-Seq
updated 3.0 years ago by 45k • written 10.2 years ago by ▴ 990
3
votes
8
replies
3.4k
views
7 follow
Non coding RNA expression data
gene-expression RNA-Seq
updated 2.2 years ago by 45k • written 9.9 years ago by ▴ 990
9
votes
13
replies
4.0k
views
What's the number at the begining of some lines of transcriptome GTF file means ?
genome-sequencing RNA-Seq Assembly genomics
updated 3.2 years ago by 45k • written 10.5 years ago by ▴ 990
22
votes
11
replies
16k
views
How to plot the heatmap of gene expression for very large data set ?
next-gen RNA-Seq R
updated 2.1 years ago by 45k • written 10.8 years ago by ▴ 990
1
vote
1
reply
1.8k
views
How to convert relative coordinate to aboulate coordinate at genome?
RNA-Seq genome next-gen R alignment
8.9 years ago by jack ▴ 990
2
votes
8
replies
6.5k
views
How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
RNA-Seq Assembly genomics Ensembl USCS
updated 8.9 years ago by 24k • written 8.9 years ago by ▴ 990
10
votes
10
replies
4.7k
views
What is best tool to call diferentially expressed isforms ?
RNA-Seq genomics R gene
updated 8.9 years ago by 7.6k • written 8.9 years ago by ▴ 990
1
vote
1
reply
2.2k
views
How to get annotation of miRNAs expression from ICGC ?
RNA-Seq mirna icgc
updated 9.0 years ago by 20 • written 9.1 years ago by ▴ 990
1
vote
1
reply
1.8k
views
non coding RNA derived from 3'-UTR
RNA-Seq RNA
updated 2.0 years ago by 45k • written 9.0 years ago by ▴ 990
2
votes
5
replies
2.0k
views
How to compare different annotation of transcriptome with each other?
RNA-Seq genomics
updated 2.0 years ago by 45k • written 9.1 years ago by ▴ 990
2
votes
2
replies
2.2k
views
How to quantify noise level of estimated isoform expression levels from RNA-seq data ?
RNA-Seq genomics
updated 2.0 years ago by 45k • written 9.1 years ago by ▴ 990
32
votes
8
replies
6.7k
views
How to write effective and stable bioinformatics pipeline in R ?
RNA-Seq pipeline software-error R
updated 3.2 years ago by 45k • written 10.5 years ago by ▴ 990
2
votes
3
replies
4.2k
views
How to map miRNA to transcripts of targeting genes ?
next-gen R RNA-Seq mirna
updated 3.2 years ago by 45k • written 10.7 years ago by ▴ 990
1
vote
2
replies
3.3k
views
Why FPKM value of gene expression profiles are very close to zero?
next-gen RNA-Seq
updated 2.1 years ago by 45k • written 9.6 years ago by ▴ 990
17
votes
4
replies
11k
views
How to get promoter coordinates of hg19 from UCSC genome browser ?
gene Assembly genomics
updated 2.6 years ago by 45k • written 9.6 years ago by ▴ 990
0
votes
1
reply
2.2k
views
What is the best human 3'-UTR annotation?
RNA-Seq sequence genomics
updated 2.6 years ago by 45k • written 9.6 years ago by ▴ 990
0
votes
1
reply
2.6k
views
What are the good tools for mRNA codon usage optimization and secondary structure prediction?
genomics
updated 2.5 years ago by 45k • written 9.7 years ago by ▴ 990
3
votes
3
replies
1.9k
views
What are the potential challegnes in non-coding transcriptome?
RNA-Seq genome
updated 2.5 years ago by 45k • written 9.7 years ago by ▴ 990
7
votes
8
replies
5.7k
views
How to extract peak coordinates for chip-seq bedgraph file ?
ChIP-Seq RNA-Seq
updated 2.5 years ago by 45k • written 9.7 years ago by ▴ 990
0
votes
4
replies
2.6k
views
why only small fraction of reads from control sample of chip-seq are mapping into the genome ?
ChIP-Seq
updated 2.4 years ago by 45k • written 9.8 years ago by ▴ 990
0
votes
1
reply
2.4k
views
Where to get human 3'-UTR multiple sequence alignment ?
alignment genome blast sequence
updated 2.3 years ago by 45k • written 9.8 years ago by ▴ 990
1
vote
7
replies
3.2k
views
looking for databases to download whole RNA RNA-seq data
ChIP-Seq RNA-Seq next-gen-sequencing
updated 2.3 years ago by 45k • written 9.8 years ago by ▴ 990
1
vote
2
replies
4.2k
views
How to compute scale bar of the dendrogram for heatmap using heatmap2 ?
R
updated 2.2 years ago by 45k • written 9.9 years ago by ▴ 990
10
votes
7
replies
8.3k
views
How much paired end vs single end RNA-seq reads can have influnce on expression level quantification ?
alignment RNA-Seq next-gen-sequencing
updated 2.2 years ago by 45k • written 9.9 years ago by ▴ 990
15
votes
26
replies
7.2k
views
How to interpret the result of GO analysis using Ontologizer / mapping GO IDs to GO TERMS ?
gene-ontology R RNA-Seq
updated 3.0 years ago by 45k • written 10.2 years ago by ▴ 990
7
votes
9
replies
9.3k
views
How to make heatmap more bright with proper color spectrum ?
heatmap genomics R
updated 2.1 years ago by 45k • written 10.2 years ago by ▴ 990
3
votes
2
replies
5.8k
views
what is the best gene ontology enrichment analysis package to include the pipeline
ontology genome RNA-Seq R
updated 3.1 years ago by 45k • written 10.3 years ago by ▴ 990
1
vote
2
replies
3.0k
views
what the best gene set enrichment analysis online tool for computing enrichement p-values ?
genome RNA-Seq R
updated 3.1 years ago by 45k • written 10.3 years ago by ▴ 990
2
votes
3
replies
5.6k
views
what is the best p value cuttoff to select differentially expressed genes ?
sequencing genomics software-error RNA-Seq
updated 3.1 years ago by 45k • written 10.3 years ago by ▴ 990
1
vote
3
replies
4.2k
views
Looking for breast cancer genes databases
genomics cancer
updated 2.9 years ago by 45k • written 10.3 years ago by ▴ 990
0
votes
1
reply
2.0k
views
How to create Gene_transcript association matrix with genome version hg19?
Assembly genome alignment R RNA-Seq
updated 3.1 years ago by 45k • written 10.3 years ago by ▴ 990
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