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1,000 results • Page 2 of 20
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35
votes
9
replies
63k
views
8 follow
Minor allele frequency calculation
SNP next-gen
updated 8 months ago by 37k • written 8.2 years ago by ▴ 50
40
votes
7
replies
62k
views
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
r rna heatmap clustering gene
updated 7 months ago by 37k • written 11.2 years ago by ▴ 450
51
votes
15
replies
62k
views
15 follow
Any Recommendations For Software For Drawing Plasmid Maps?
visualization software
updated 9 months ago by 37k • written 11.6 years ago by ▴ 70
53
votes
4
replies
59k
views
What is difference between soft-clipped and hard-clipped in SAM specification?
sequence next-gen-sequencing
updated 3 months ago by 37k • written 8.2 years ago by ▴ 780
102
votes
30
replies
59k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment tool
updated 7 months ago by 37k • written 12.9 years ago by ★ 1.0k
152
votes
24
replies
58k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
splicing tools rna-seq alternative-splicing
updated 6 months ago by 37k • written 9.9 years ago by 10k
2
votes
10
replies
58k
views
R: remove rows by a list of rownames
R
updated 9 months ago by 37k • written 8.0 years ago by ▴ 50
146
votes
35
replies
57k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 8 months ago by • 0 • written 10.2 years ago by ★ 1.6k
361
votes
57
replies
57k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 4 months ago by 84k • written 12.9 years ago by 96k
91
votes
25
replies
57k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks selection software
updated 4 months ago by 52k • written 11.9 years ago by 3.4k
90
votes
44
replies
57k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 9 months ago by 37k • written 11.8 years ago by ★ 3.4k
328
votes
54
replies
56k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 4 months ago by 84k • written 12.9 years ago by 24k
11
votes
9
replies
56k
views
7 follow
combining fasta files
windows fasta notepad
updated 10 weeks ago by • 0 • written 8.0 years ago by ▴ 30
87
votes
18
replies
55k
views
12 follow
Sequence length from Fasta
fasta
updated 5 weeks ago by 37k • written 8.2 years ago by ▴ 80
93
votes
19
replies
55k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
tree tool phylogenetics viewer
updated 8 months ago by ▴ 20 • written 12.4 years ago by ★ 2.6k
49
votes
20
replies
55k
views
14 follow
Bam Header Edit
bam
updated 5 months ago by 37k • written 10.7 years ago by 12k
24
votes
10
replies
55k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
Tutorial error software R
updated 8 months ago by • 0 • written 22 months ago by ★ 1.3k
38
votes
20
replies
54k
views
8 follow
How to convert to .SRA files to .FQ (FASTQ)
fastq FASTQ sra RNA-Seq SRAA
updated 11 months ago by ▴ 20 • written 8.5 years ago by ▴ 50
62
votes
22
replies
54k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf bed
updated 7 weeks ago by • 0 • written 10.2 years ago by ★ 1.5k
78
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
tutorial Tutorial
written 9.6 years ago by 11k
45
votes
14
replies
52k
views
10 follow
Tutorial: Using R in Conda
R Tutorial
updated 12 weeks ago by ▴ 20 • written 2.5 years ago by ▴ 690
74
votes
24
replies
51k
views
16 follow
How To Sort Bed Format File
bed
updated 3 months ago by 152k • written 9.9 years ago by ▴ 430
126
votes
33
replies
51k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 3 months ago by 37k • written 8.8 years ago by ▴ 480
143
votes
34
replies
51k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
mutation maf tcga cancer music Tutorial
updated 8 months ago by 37k • written 9.8 years ago by 5.8k
27
votes
8
replies
50k
views
7 follow
R: How to convert log2FC (Fold Change) obtained by limma's topTable() function to FC
limma microarray topTable R
updated 6 months ago by 37k • written 8.7 years ago by ★ 4.0k
75
votes
22
replies
49k
views
17 follow
How To Download All Sra Samples At Once ?
geo download sra
updated 10 months ago by ▴ 90 • written 8.9 years ago by ★ 1.5k
77
votes
27
replies
48k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 5 months ago by ▴ 70 • written 9.1 years ago by ▴ 180
1.2k
votes
205
replies
47k
views
107 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 11 days ago by ▴ 240 • written 11.8 years ago by 21k
87
votes
37
replies
47k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 10 months ago by 37k • written 9.5 years ago by ▴ 110
45
votes
3
replies
47k
views
Gwas Vs. Qtl Mapping?
gwas mapping
updated 7 months ago by 37k • written 10.6 years ago by ▴ 460
54
votes
22
replies
47k
views
14 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 6 months ago by 34k • written 9.9 years ago by ★ 1.2k
57
votes
15
replies
46k
views
11 follow
Filtering Vcf File
vcftools vcf snp indel
updated 11 months ago by 37k • written 10.4 years ago by ▴ 830
65
votes
17
replies
46k
views
15 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq tools
updated 4 weeks ago by 37k • written 10.0 years ago by ★ 3.6k
42
votes
11
replies
45k
views
10 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 5 months ago by 37k • written 7.1 years ago by ▴ 460
112
votes
24
replies
44k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 5 months ago by 37k • written 11.7 years ago by ▴ 480
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 8 months ago by 37k • written 7.9 years ago by ★ 2.0k
32
votes
19
replies
43k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene convert
updated 4 weeks ago by 37k • written 9.7 years ago by ▴ 240
77
votes
18
replies
43k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 6 months ago by • 0 • written 12.7 years ago by ★ 1.1k
48
votes
4
replies
42k
views
How To Convert The Bed File To Ped File
bed ped
updated 4 months ago by • 0 • written 12.4 years ago by ▴ 310
31
votes
7
replies
42k
views
6 follow
Using transcripts per million (TPM)
RNA-Seq deseq2 tpm
updated 6 months ago by 37k • written 7.9 years ago by ▴ 170
39
votes
16
replies
42k
views
10 follow
How to split paired end SRA file into 2 correct fastq files
next-gen sra fastq
updated 11 months ago by ▴ 10 • written 6.2 years ago by ▴ 120
142
votes
68
replies
42k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
updated 7 months ago by • 0 • written 5.2 years ago by 84k
32
votes
10
replies
41k
views
8 follow
Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
tophat illumina strand
updated 3 months ago by 37k • written 9.9 years ago by 10k
116
votes
74
replies
41k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 12 weeks ago by 125k • written 12.1 years ago by ★ 3.2k
31
votes
11
replies
41k
views
9 follow
How To Sort Sam File
samtools sam
updated 19 days ago by 37k • written 8.9 years ago by ★ 1.1k
51
votes
19
replies
41k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
chip-seq rna-seq bigwig visualization ucsc tutorial Tutorial
updated 6 months ago by 37k • written 10.8 years ago by 11k
292
votes
27
replies
41k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 6 months ago by 37k • written 7.0 years ago by ★ 2.4k
34
votes
15
replies
41k
views
8 follow
FPKM vs raw counts vs RPKM
counts rpkm raw fpkm RNA-Seq
updated 10 months ago by 37k • written 8.1 years ago by ▴ 330
3
votes
5
replies
41k
views
how to set the size of cell of heatmap.2 in R
heatmap.2 R
updated 11 months ago by 37k • written 8.2 years ago by ★ 2.1k
38
votes
14
replies
41k
views
7 follow
Extraction Of Header Of Sequences In Fasta File
perl fasta python parsing
updated 9 months ago by 52k • written 11.1 years ago by ▴ 350
1,000 results • Page 2 of 20
Recent Votes
A: Using ColSums vs sizeFactors in read count normalization
Comment: a problem with getBM
C: Reorder heatmap rows in a dataset with missing values
A: Difference between GTF file with CHR and without CHR. ENSEMBL
Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
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Teacher to ATpoint 68k
Popular Question to tianshenbio ▴ 160
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Recent Replies
Answer: how to do a reliable single cell sequencing analysis? by ATpoint 68k
The usual approach for starters would be to follow guided and well-accepted tutorials. That would (incomplete list) be: - The Biocon…
Answer: a problem with getBM by sanaz • 0
head(ensembl_ids) X baseMean log2FoldChange lfcSE stat pvalue padj 1 ENSG00000000938.13 1344.2587 2.107…
Answer: Recommendations needed for a tool for comparative gene set enrichment analyses v by fuellen ▴ 20
Hello and Thanks! OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared". In any case, is …
Comment: a problem with getBM by Mike Smith ★ 1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`. It's …
Answer: trainGlimmerHMM Error while training a genome by congliu37 • 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File? by Jeremy Leipzig 21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)? by Fabio Marroni ★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism by Rob ▴ 160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers by Pierre Lindenbaum 152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence by vvasta • 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation? by Fabio Marroni ★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2 by Fabio Marroni ★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file** by Pierre Lindenbaum 152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
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