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3
votes
14
replies
1.2k
views
How to extract specific region from multiple bam files and merge the outputs into single bam?
bam rna-seq
updated 6 months ago by 142k • written 6 months ago by ▴ 770
3
votes
3
replies
1.4k
views
How to remove uncharacterized chromosomes from GTF file?
grep gtf awk
updated 15 months ago by 11k • written 15 months ago by ▴ 770
2
votes
8
replies
1.5k
views
How to subset a gtf based on names in the third column of another file in a single command?
grep rnaseq awk
updated 20 months ago by 142k • written 20 months ago by ▴ 770
1
vote
4
replies
754
views
How to read fastqs from different sequencing runs rather than merging?
ngs rnaseq fastq
updated 2.0 years ago by ★ 5.9k • written 2.0 years ago by ▴ 770
12
votes
12
replies
13k
views
7 follow
Gene set enrichment analysis with logFC and PValue
RNA-Seq gsea r gene expression genesetenrichment
updated 3.3 years ago by ▴ 110 • written 5.6 years ago by ▴ 770
19
votes
5
replies
18k
views
6 follow
showing specific GO pathways in the dotplot or cnetplot
RNA-Seq R clusterprofiler dotplot goenrichment
updated 3.0 years ago by ▴ 10 • written 5.3 years ago by ▴ 770
5
votes
6
replies
2.5k
views
Question about WGCNA Module Eigengenes to Pathway analysis
RNA-Seq wgcna geneexpression coexpressionnetwork
updated 4.0 years ago by 3.6k • written 4.0 years ago by ▴ 770
1
vote
1
reply
884
views
Identification of transcription factor - gene regulation information
RNA-Seq tcga transcription factor
updated 4.4 years ago by 20 • written 5.0 years ago by ▴ 770
1
vote
4
replies
1.4k
views
Different miRNAs with same miRNA regions in TCGA
tcga mirna mirtarbase mirnaseq
4.6 years ago by Vasu ▴ 770
8
votes
3
replies
1.6k
views
Question about Isoform expression (miRNA) data from TCGA
mirna mirnaseq mirbase mirtarbase tcga
updated 4.6 years ago by 19k • written 4.6 years ago by ▴ 770
17
votes
8
replies
2.1k
views
Question about miRNA nomenclature
mirna mirnaseq mirbase
updated 2.3 years ago by 19k • written 4.6 years ago by ▴ 770
3
votes
1
reply
8.7k
views
Ensembl id to GeneSymbol with biomart
biomart
updated 4.8 years ago by 20 • written 6.7 years ago by ▴ 770
11
votes
10
replies
2.1k
views
Question about differentially expressed genes selection for low sample size data
RNA-Seq R geneexpression edger pvalue
updated 5.0 years ago by ★ 1.3k • written 5.0 years ago by ▴ 770
3
votes
6
replies
1.2k
views
Question about chromosomal instability
copy number chromosome gene R genome
updated 5.0 years ago by 87k • written 5.0 years ago by ▴ 770
34
votes
35
replies
17k
views
8 follow
Sample names for TCGA data from GDC-legacy archive
RNA-Seq tcga gdc
updated 5.2 years ago by ▴ 30 • written 6.1 years ago by ▴ 770
2
votes
7
replies
2.0k
views
Question about ClinicalData discrepancies b/w cbioportal data and GDC data?
survival gdc cbioportal tcga clinicaldata
5.2 years ago by Vasu ▴ 770
4
votes
4
replies
3.0k
views
Error with merge_result with dataframes using clusterprofiler
R clusterprofiler RNA-Seq enrichment
5.2 years ago by Vasu ▴ 770
1
vote
2
replies
2.0k
views
How to get correlation coefficient value between the genes in the WGCNA module network?
RNA-Seq wgcna coexpressionnetwork R lncrna
5.2 years ago by Vasu ▴ 770
3
votes
7
replies
2.2k
views
Differential analysis with replicates using edgeR
RNA-Seq edger differential analysis design matrix
updated 5.4 years ago by 20 • written 5.4 years ago by ▴ 770
3
votes
8
replies
2.5k
views
Correlation between lncRNA and protein coding genes
RNA-Seq R correlation lncRNA genes
updated 5.5 years ago by 11k • written 5.5 years ago by ▴ 770
2
votes
9
replies
2.5k
views
Is TCGA Breast cancer data strand specific?
RNA-Seq tcga strand geneexpression hisat2
updated 5.5 years ago by 142k • written 5.5 years ago by ▴ 770
6
votes
8
replies
2.7k
views
How to bring consistency for genome reference, annotation and index files?
RNA-Seq hisat2 genome gencode annotation
5.6 years ago by Vasu ▴ 770
2
votes
8
replies
3.7k
views
FPKM matrix after stringtie using ballgown
RNA-Seq stringtie ballgown fpkm
updated 5.7 years ago by ★ 2.6k • written 5.7 years ago by ▴ 770
7
votes
5
replies
2.9k
views
Expression of a gene across all cancer datasets
RNA-Seq r tcga geneexpression cancer
updated 2.9 years ago by 142k • written 5.8 years ago by ▴ 770
16
votes
17
replies
7.9k
views
Samples with same TCGA barcode in TCGA data
RNA-Seq tcga gdc
updated 5.8 years ago by ▴ 100 • written 6.1 years ago by ▴ 770
3
votes
7
replies
1.6k
views
Expression of specific genes between tumor and normal
RNA-Seq differential analysis r rna
updated 5.8 years ago by 11k • written 5.8 years ago by ▴ 770
0
votes
6
replies
2.1k
views
Subsampling procedure for differential analysis
RNA-Seq R differential analysis rna
5.8 years ago by Vasu ▴ 770
1
vote
5
replies
4.4k
views
How to make a scatter plot showing correlation between genes?
RNA-Seq scatterplot gene rpkm r
5.8 years ago by Vasu ▴ 770
1
vote
16
replies
2.0k
views
Why I see very high mapping percentage, Is this normal or anything wrong in generating libraries?
RNA-Seq hisat2 samtools mapping
updated 5.9 years ago by 20 • written 6.0 years ago by ▴ 770
14
votes
8
replies
28k
views
Adding column annotation to heatmap using Complexheatmap
RNA-Seq r heatmap complexheatmap
updated 5.9 years ago by 87k • written 5.9 years ago by ▴ 770
1
vote
12
replies
3.5k
views
How to make a PCA plot to check similar samples between two cohorts?
RNA-Seq microarray pca z-score
updated 5.9 years ago by 87k • written 5.9 years ago by ▴ 770
0
votes
1
reply
1.6k
views
Salmon tool giving an error about the library type
RNA-Seq salmon alignment rna library
5.9 years ago by Vasu ▴ 770
7
votes
17
replies
5.6k
views
Duplicate samples in TCGA Breast cancer data. Which one to pick?
RNA-Seq tcga breast gdc
6.0 years ago by Vasu ▴ 770
3
votes
3
replies
2.9k
views
How to separate protein-coding and non-coding in gtf file
RNA-Seq gtf proteincoding noncoding lncrna
updated 6.0 years ago by 11k • written 6.0 years ago by ▴ 770
4
votes
6
replies
2.7k
views
Why difference in Hisat2 and bamqc from qualimap results?
RNA-Seq hisat2 qualimap bamqc
updated 6.0 years ago by 20 • written 6.0 years ago by ▴ 770
3
votes
6
replies
4.0k
views
Samtools sort error with a bam file
RNA-Seq samtools sort bam
updated 6.1 years ago by 104k • written 6.1 years ago by ▴ 770
0
votes
12
replies
6.8k
views
Creating Hisat2 Index
RNA-Seq hisat2 genome index
6.2 years ago by Vasu ▴ 770
18
votes
20
replies
14k
views
Which strand specific option need to be used with HISAT2?
RNA-Seq hisat2 strandspecific
updated 16 months ago by ★ 5.1k • written 6.2 years ago by ▴ 770
4
votes
6
replies
4.6k
views
How to get the simple somatic mutation vcf file from GDC data portal?
gdc mutations vcf maf tcgabiolinks
6.3 years ago by Vasu ▴ 770
2
votes
5
replies
5.9k
views
How to change colors for each column in the heatmap using "complexheatmap" package?
R complexheatmap bioconductor heatmap
updated 6.3 years ago by 87k • written 6.3 years ago by ▴ 770
1
vote
7
replies
7.1k
views
How to convert gtf to bed format
gtf bed
6.3 years ago by Vasu ▴ 770
3
votes
7
replies
3.3k
views
Why different rna-seq aligners need to be used for Ion Torrent data compared with illumina?
RNA-Seq tophat hisat2 bbmap mira
updated 6.3 years ago by 35k • written 6.3 years ago by ▴ 770
0
votes
9
replies
3.0k
views
SnpSift doesn't show any VariantType for filtering
snpeff snpsift filtering mutations
updated 6.3 years ago by 20 • written 6.4 years ago by ▴ 770
5
votes
18
replies
8.2k
views
Bam to read counts for differential expression analysis
RNA-Seq bam expression analysis
updated 6.4 years ago by ▴ 50 • written 6.4 years ago by ▴ 770
3
votes
6
replies
2.6k
views
Annotation of VCF file
vcf mutation snpeff
updated 6.4 years ago by 47k • written 6.4 years ago by ▴ 770
3
votes
6
replies
10k
views
Differential expression analysis for log2(x+1) transformed RSEM normalized count (TCGA)
r RNA-Seq differential analysis tcga
updated 7.0 years ago by • 0 • written 7.0 years ago by ▴ 770
5
votes
4
replies
9.4k
views
How to build Hisat2 index for human genome (GRCh37 )?
RNA-Seq hisat2
updated 7.0 years ago by 35k • written 7.0 years ago by ▴ 770
0
votes
1
reply
1.5k
views
subclass mapping algorithm for subclassing independent datasets
cancer submap classification
updated 12 months ago by 43k • written 7.2 years ago by ▴ 770
10
votes
13
replies
5.8k
views
How to identify DE lncRNA from RNA Seq Data?
RNA-Seq lncrna
7.2 years ago by Vasu ▴ 770
3
votes
4
replies
6.9k
views
How to perform Fisher's exact test between two gene lists for a particular gene in R?
R fishers test significance statistics
updated 7.3 years ago by ▴ 180 • written 7.3 years ago by ▴ 770
55 results • Page 1 of 2
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