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1,000 results • Page 5 of 20
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17
votes
5
replies
44k
views
Scale Data Before Drawing Heatmap Or Using Heatmap(..., Scale="Columan") In R?
heatmap r
updated 11.5 years ago by 52k • written 11.5 years ago by ▴ 140
27
votes
15
replies
43k
views
16 follow
how to unzip the files in batch?
next-gen RNA-Seq SNP alignment
updated 3 months ago by 39k • written 8.1 years ago by ▴ 50
63
votes
8
replies
43k
views
6 follow
Why Do You Need To Use Cdna For Rna-Seq?
rna-seq cdna
updated 6.8 years ago by • 0 • written 10.6 years ago by ▴ 460
31
votes
7
replies
43k
views
6 follow
Using transcripts per million (TPM)
RNA-Seq deseq2 tpm
updated 10 months ago by 39k • written 8.2 years ago by ▴ 170
38
votes
14
replies
43k
views
7 follow
Extraction Of Header Of Sequences In Fasta File
perl fasta python parsing
updated 13 months ago by 52k • written 11.4 years ago by ▴ 350
78
votes
16
replies
43k
views
11 follow
How do you cite a tool that doesn't have a publication?
citation academic style
updated 7.1 years ago by 23k • written 7.2 years ago by ★ 1.1k
9
votes
7
replies
43k
views
R programming: compare columns to column and get the mismatch
R
updated 3 months ago by 39k • written 8.1 years ago by ★ 2.0k
32
votes
10
replies
43k
views
8 follow
Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
tophat illumina strand
updated 7 months ago by 39k • written 10.3 years ago by 10k
61
votes
22
replies
43k
views
7 follow
extract dendrogram cluster from pheatmap
R
updated 15 months ago by • 0 • written 5.5 years ago by ★ 1.1k
25
votes
23
replies
43k
views
12 follow
How To Generate A Consensus Fasta Sequence From Sam Tools Pileup?
samtools next-gen sequencing fasta
updated 9.3 years ago by ▴ 180 • written 13.0 years ago by 18k
25
votes
6
replies
42k
views
Aggregate multiple rows based on common values in given columns
R
updated 4.7 years ago by 11k • written 7.5 years ago by ▴ 70
117
votes
74
replies
42k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 7 months ago by 129k • written 12.5 years ago by ★ 3.3k
30
votes
14
replies
42k
views
9 follow
Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files
rna-seq differential expression
updated 7.0 years ago by 20 • written 11.1 years ago by ▴ 310
49
votes
10
replies
42k
views
When and why is bwa aln better then bwa mem?
aln comparison bwa mem
updated 2.2 years ago by 39k • written 8.6 years ago by 14k
11
votes
8
replies
42k
views
Converting Smiles To Iupac Chemical Name?
updated 10.9 years ago by 5.4k • written 10.9 years ago by ▴ 730
31
votes
11
replies
42k
views
9 follow
How To Sort Sam File
samtools sam
updated 4 months ago by 39k • written 9.3 years ago by ★ 1.1k
294
votes
27
replies
42k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 10 months ago by 39k • written 7.3 years ago by ★ 2.4k
79
votes
6
replies
42k
views
6 follow
Read Group In Sam/Bam Files: What Do They Exactly Describe?
bam samtools next-gen
updated 14 months ago by 39k • written 11.1 years ago by 4.3k
3
votes
5
replies
42k
views
how to set the size of cell of heatmap.2 in R
heatmap.2 R
updated 15 months ago by 39k • written 8.5 years ago by ★ 2.1k
51
votes
19
replies
42k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 3 months ago by 39k • written 11.1 years ago by 11k
2
votes
4
replies
42k
views
python 3.8 'No module named pip'
rna-seq
updated 23 months ago by ▴ 10 • written 2.9 years ago by • 0
4
votes
1
reply
42k
views
ggmaplot error: Unlabeled data points (too many overlaps). Consider increasing max.overlaps
MAplot r ggplot2 ggmaplot
updated 22 months ago by 72k • written 2.3 years ago by ▴ 110
34
votes
15
replies
41k
views
8 follow
FPKM vs raw counts vs RPKM
counts rpkm raw fpkm RNA-Seq
updated 14 months ago by 39k • written 8.4 years ago by ▴ 330
40
votes
4
replies
41k
views
What Is Snp Calling?
snp next-gen sequencing snp
updated 12.4 years ago by • 0 • written 13.1 years ago by 27k
63
votes
16
replies
41k
views
11 follow
How To Analyze Imputed Gwas Data
gwas r snp imputation plink
updated 2.9 years ago by ▴ 70 • written 12.2 years ago by 2.8k
32
votes
8
replies
41k
views
7 follow
Difference Between "Pipeline" And "Workflow" ?
next-gen sequencing
written 11.3 years ago by ★ 1.5k
26
votes
9
replies
41k
views
How Logfc Value Is Calculated In Edger?
edger r RNA-seq
updated 3 months ago by 39k • written 9.7 years ago by ▴ 240
68
votes
14
replies
41k
views
9 follow
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
risk minor major reference alleles
updated 23 months ago by 85k • written 5.1 years ago by ▴ 400
134
votes
27
replies
41k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 13 months ago by 39k • written 11.1 years ago by 33k
116
votes
66
replies
41k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 11 weeks ago by 39k • written 4.9 years ago by 72k
48
votes
33
replies
41k
views
16 follow
Extract A Group Of Fasta Sequences From A File
fasta python perl biopython bioperl
updated 17 months ago by 39k • written 12.9 years ago by ▴ 60
9
votes
16
replies
41k
views
6 follow
Beginner in Python- need in assistance translating DNA into protein sequence
python
updated 2.3 years ago by • 0 • written 6.5 years ago by ▴ 10
14
votes
6
replies
41k
views
Does Anyone Know How To Cite Ncbi Wwwblast In A Manuscript?
ncbi
updated 9.8 years ago by ▴ 180 • written 9.8 years ago by ▴ 830
39
votes
17
replies
41k
views
13 follow
Extract Cds Fastas From A Gff Annotation + Reference Sequence
gff CDS
updated 3 months ago by 39k • written 11.0 years ago by ▴ 700
1
vote
3
replies
40k
views
Error in loading R package "GO.db" in installing WGCNA R package
R
updated 12 months ago by 39k • written 8.2 years ago by ▴ 10
5
votes
7
replies
40k
views
PLINK: merge .bed files
plink
updated 5 months ago by 39k • written 7.9 years ago by ▴ 230
20
votes
8
replies
40k
views
Convert .Txt File To Bed File
bed
updated 8.9 years ago by ▴ 220 • written 11.7 years ago by ★ 1.7k
109
votes
56
replies
40k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 8 months ago by 39k • written 11.0 years ago by ▴ 380
22
votes
4
replies
40k
views
Convert plink files to VCF: Reference allele file
SNP genome
updated 8 months ago by 39k • written 7.8 years ago by ▴ 70
33
votes
11
replies
40k
views
8 follow
Where Can I Download Some Bam Files?
bam RNA-seq
updated 3 months ago by 39k • written 11.0 years ago by ▴ 160
46
votes
9
replies
40k
views
9 follow
How To Convert Centimorgan To Base Pair
genetics distance
updated 8 months ago by 39k • written 11.4 years ago by ▴ 90
25
votes
9
replies
40k
views
Converting Gff To Bed With Bedtools?
bedtools gff bed conversion
updated 10.4 years ago by 35k • written 10.4 years ago by ▴ 930
42
votes
21
replies
40k
views
11 follow
Comparing 2 Large Lists (Millions Of Rows) To Identify Shared And Exclusive Elements
unix list intersect
updated 18 months ago by 39k • written 10.3 years ago by ▴ 620
6
votes
7
replies
40k
views
6 follow
Bowtie Building Index Issue
bowtie bowtie2 genome
updated 11.0 years ago by 98k • written 11.0 years ago by ▴ 40
29
votes
5
replies
40k
views
What Does Up-Regulated And Down-Regulated Mean？
updated 17 months ago by • 0 • written 11.1 years ago by ▴ 100
6
votes
11
replies
40k
views
Finding The Mean Of Values In A Single Column
r
updated 9.6 years ago by 52k • written 9.6 years ago by ▴ 110
21
votes
14
replies
40k
views
7 follow
Gene symbol convert to Entrez ID
Entrez R biomart
updated 4.7 years ago by 11k • written 6.0 years ago by ▴ 180
85
votes
19
replies
40k
views
17 follow
How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
assembly quality next-gen
updated 15 months ago by ▴ 10 • written 10.4 years ago by ▴ 470
50
votes
21
replies
40k
views
11 follow
How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?
rpkm rna-seq cutoff fpkm
updated 18 months ago by 39k • written 10.4 years ago by ★ 1.5k
38
votes
11
replies
40k
views
7 follow
In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
seurat single-cell
updated 19 months ago by ★ 14k • written 3.6 years ago by ▴ 760
1,000 results • Page 5 of 20
Recent Votes
C: PLINK logistic regression analysis and covariates
Comment: Regular Expression for conversion
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
A: PolyPhen Humdiv vs HumVar discrepancies
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Recent Replies
Comment: Unusual FASTQ file by Ram 39k
People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more…
Comment: How to make a dotplot for bulk RNA average expression ? by bhumm ▴ 40
I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
Answer: What is the best way to clean bulk RNA-seq data? by swbarnes2 13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data? by Vincent Laufer ★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file by bhumm ▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline by ATpoint 72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline by swbarnes2 13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline by Ram 39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline by turcoa1 • 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline by Ram 39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline by turcoa1 • 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree by GenoMax 129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline by Ram 39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index by ashleymb1116 • 0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index by GenoMax 129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
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