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116,882 results • Page 5 of 2338
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30
votes
10
replies
48k
views
Filtering A Sam File For Quality Scores
sam
updated 12.0 years ago by 11k • written 12.0 years ago by ★ 1.3k
4
votes
1
reply
48k
views
In ggplot, assign a variable/category to a specific color?
R ggplot plots colors
updated 7.6 years ago by 20 • written 7.8 years ago by ▴ 100
24
votes
14
replies
48k
views
7 follow
Gene symbol convert to Entrez ID
Entrez R biomart
updated 5.7 years ago by 11k • written 6.9 years ago by ▴ 190
39
votes
14
replies
48k
views
7 follow
Extraction Of Header Of Sequences In Fasta File
perl fasta python parsing
updated 2.1 years ago by 54k • written 12.4 years ago by ▴ 350
3
votes
5
replies
48k
views
Convert text file to VCF file ?
vcf
updated 10 months ago by 43k • written 9.2 years ago by ▴ 280
32
votes
8
replies
47k
views
7 follow
Difference Between "Pipeline" And "Workflow" ?
next-gen sequencing
written 12.2 years ago by ★ 1.5k
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene
updated 10 months ago by 43k • written 11.0 years ago by ▴ 250
22
votes
4
replies
47k
views
Convert plink files to VCF: Reference allele file
SNP genome
updated 19 months ago by 43k • written 8.7 years ago by ▴ 70
6
votes
12
replies
47k
views
9 follow
Opening A Fasta File In Windows
fasta blast makeblastdb
updated 12.2 years ago by • 0 • written 12.2 years ago by • 0
49
votes
4
replies
47k
views
How To Convert The Bed File To Ped File
bed ped
updated 20 months ago by • 0 • written 13.7 years ago by ▴ 310
112
votes
24
replies
47k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 20 months ago by 43k • written 13.0 years ago by ▴ 480
100
votes
106
replies
47k
views
26 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 4 weeks ago by ▴ 20 • written 5.7 years ago by 87k
57
votes
23
replies
46k
views
14 follow
Bam File: Change Chromosome Notation
samtools bam
updated 3.0 years ago by 11k • written 12.6 years ago by ▴ 160
118
votes
74
replies
46k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 18 months ago by 142k • written 13.4 years ago by ★ 3.3k
117
votes
66
replies
46k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 14 months ago by 43k • written 5.9 years ago by 82k
77
votes
18
replies
46k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 21 months ago by • 0 • written 14.0 years ago by ★ 1.1k
9
votes
12
replies
46k
views
8 follow
Tools to view fastq file
fastq
updated 10 months ago by 43k • written 8.0 years ago by ▴ 40
17
votes
5
replies
46k
views
Scale Data Before Drawing Heatmap Or Using Heatmap(..., Scale="Columan") In R?
heatmap r
updated 12.4 years ago by 54k • written 12.4 years ago by ▴ 140
11
votes
8
replies
46k
views
Converting Smiles To Iupac Chemical Name?
updated 11.8 years ago by 5.4k • written 11.8 years ago by ▴ 730
81
votes
6
replies
46k
views
6 follow
Read Group In Sam/Bam Files: What Do They Exactly Describe?
bam samtools next-gen
updated 2.1 years ago by 43k • written 12.0 years ago by 4.4k
49
votes
10
replies
45k
views
When and why is bwa aln better then bwa mem?
aln comparison bwa mem
updated 3.1 years ago by 43k • written 9.5 years ago by 14k
298
votes
27
replies
45k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 21 months ago by 43k • written 8.3 years ago by ★ 2.4k
32
votes
7
replies
45k
views
6 follow
Using transcripts per million (TPM)
RNA-Seq deseq2 tpm
updated 22 months ago by 43k • written 9.2 years ago by ▴ 170
22
votes
7
replies
45k
views
Extracting cells only from one condition (Seurat)
single cell rnaseq seurat RNA-Seq R
updated 3.0 years ago by ▴ 50 • written 4.3 years ago by ▴ 380
30
votes
14
replies
45k
views
9 follow
Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files
rna-seq differential expression
updated 7.9 years ago by 20 • written 12.0 years ago by ▴ 310
35
votes
11
replies
45k
views
8 follow
Where Can I Download Some Bam Files?
bam RNA-seq
updated 4 months ago by 43k • written 12.0 years ago by ▴ 160
134
votes
27
replies
45k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 2.1 years ago by 43k • written 12.1 years ago by 33k
32
votes
11
replies
45k
views
9 follow
How To Sort Sam File
samtools sam
updated 16 months ago by 43k • written 10.2 years ago by ★ 1.1k
25
votes
23
replies
44k
views
12 follow
How To Generate A Consensus Fasta Sequence From Sam Tools Pileup?
samtools next-gen sequencing fasta
updated 10.3 years ago by ▴ 180 • written 13.9 years ago by 18k
23
votes
8
replies
44k
views
Convert .Txt File To Bed File
bed
updated 9.9 years ago by ▴ 260 • written 12.7 years ago by ★ 1.7k
25
votes
9
replies
44k
views
Converting Gff To Bed With Bedtools?
gff bed bedtools
updated 3 months ago by 43k • written 11.3 years ago by ▴ 940
17
votes
3
replies
44k
views
What'S The Meaning Of "Bridge Pcr" In The Next Generation Sequencing
pcr sequencing
updated 10.9 years ago by ★ 5.3k • written 10.9 years ago by ▴ 150
63
votes
8
replies
44k
views
6 follow
Why Do You Need To Use Cdna For Rna-Seq?
rna-seq cdna
updated 7.7 years ago by • 0 • written 11.6 years ago by ▴ 460
5
votes
3
replies
44k
views
Extract the values by matching two rows of one dataframe with the two columns of another dataframe
dataframe match
updated 24 months ago by 43k • written 9.2 years ago by ★ 2.1k
112
votes
56
replies
44k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 20 months ago by 43k • written 12.0 years ago by ▴ 380
32
votes
10
replies
44k
views
8 follow
Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
tophat illumina strand
updated 19 months ago by 43k • written 11.2 years ago by 11k
85
votes
19
replies
44k
views
17 follow
How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
assembly quality next-gen
updated 2.3 years ago by ▴ 10 • written 11.3 years ago by ▴ 470
48
votes
9
replies
44k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 3 months ago by ▴ 640 • written 7.5 years ago by ▴ 570
32
votes
5
replies
44k
views
What is Differential Expression?
DNA genes
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 50
35
votes
14
replies
44k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf bcftools
updated 7 months ago by ▴ 130 • written 7.8 years ago by ★ 5.3k
3
votes
5
replies
44k
views
how to set the size of cell of heatmap.2 in R
heatmap.2 R
updated 2.2 years ago by 43k • written 9.4 years ago by ★ 2.2k
60
votes
52
replies
44k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 14 months ago by 43k • written 7.6 years ago by ★ 3.5k
53
votes
19
replies
44k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 14 months ago by 43k • written 12.1 years ago by 11k
37
votes
15
replies
44k
views
8 follow
FPKM vs raw counts vs RPKM
counts rpkm raw fpkm RNA-Seq
updated 2.2 years ago by 43k • written 9.4 years ago by ▴ 360
121
votes
35
replies
44k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 12 months ago by 43k • written 6.9 years ago by ▴ 810
26
votes
9
replies
44k
views
How Logfc Value Is Calculated In Edger?
edger r RNA-seq
updated 14 months ago by 43k • written 10.6 years ago by ▴ 240
9
votes
7
replies
43k
views
R programming: compare columns to column and get the mismatch
R
updated 15 months ago by 43k • written 9.0 years ago by ★ 2.1k
14
votes
6
replies
43k
views
Does Anyone Know How To Cite Ncbi Wwwblast In A Manuscript?
ncbi
updated 10.8 years ago by ▴ 180 • written 10.8 years ago by ▴ 830
46
votes
9
replies
43k
views
7 follow
Tool: Tools to merge overlapping paired-end reads
ngs Assembly fastq
updated 13 months ago by ▴ 50 • written 7.4 years ago by ★ 1.2k
18
votes
21
replies
43k
views
11 follow
R org.Hs.eg.db matching ensembl gene ids with gene symbol
bioconductor R
updated 2.6 years ago by ▴ 10 • written 8.2 years ago by ▴ 330
116,882 results • Page 5 of 2338
Recent Votes
Comment: Longest transcript variant per gene
Comment: Longest transcript variant per gene
Answer: Longest transcript variant per gene
Answer: Longest transcript variant per gene
Comment: Longest transcript variant per gene
Comment: Longest transcript variant per gene
Answer: install package
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Recent Replies
Answer: input file in rmats by Mathew ▴ 90
Hi, In the example they give in their GitHub (https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/README.md): They have 2 sample groups wi…
Comment: Longest transcript variant per gene by Mathew ▴ 90
I'm glad it worked well for you! Good luck with the rest of your project. I wish you the best.
Comment: Longest transcript variant per gene by sansan_96 ▴ 90
Thanks so much
Comment: Longest transcript variant per gene by sansan_96 ▴ 90
Hello again, It works very well, thank you very much for this solution.
Comment: Longest transcript variant per gene by sansan_96 ▴ 90
Hello Mathew, Thanks for your answer, I'll try it and come back.
Answer: Longest transcript variant per gene by Mathew ▴ 90
Hi, why not write code to extract the longest variant? I copied these two in a txt file called "input.txt", and made three dummy variants …
Comment: Longest transcript variant per gene by GenoMax 142k
https://www.biostars.org/p/107759/<br> https://www.biostars.org/p/403649/ <!-- this is it -->
Answer: Kraken2 database by Mathew ▴ 90
Sorry, what analysis are you trying to perform with these databases? Based on your question, it appears you are using Kraken2 and Bracken.…
Comment: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike by Mathew ▴ 90
I looked up a publication using CIBERSORT to see how they got the package, and indeed they acquired it through official website application…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py by fracarb8 ★ 1.6k
If you are using R, you should check the liana R implementation (https://github.com/saezlab/liana).
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by ajbarrett98 • 0
Thank you Pierre, I am going to take some time to get my head around this and report back if it works.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by ajbarrett98 • 0
Thanks for the crosspost! Just trying to get things figured out.
Answer: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike by ATpoint 82k
To the best of my knowledge, CIBERSORT is and has always and only been available via the official website application from Stanford. Whatev…
Comment: BioLabDonkey - new Mac program for molecular biologists by vytarasov ▴ 180
Update of BioLabDonkey - Version 5.6 - In silico PCR function is added.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by Pierre Lindenbaum 161k
cross posted: https://stackoverflow.com/questions/78462732/ > Please mind that posting the same question to multiple sites can be perceive…
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