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12,517 results • Page 3 of 251
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87
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24
replies
24k
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17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 4 weeks ago by • 0 • written 3.6 years ago by 3.2k
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 6 months ago by 44k • written 14.1 years ago by 28k
20
votes
24
replies
7.0k
views
6 follow
Forum: Python or R
RNA-Seq alignment next-gen-sequencing
updated 12 months ago by 44k • written 6.0 years ago by ▴ 160
27
votes
24
replies
2.5k
views
7 follow
Code Golf - bisulfite conversion
bisulfite bsseq code-golf
updated 12 months ago by 44k • written 5.6 years ago by 22k
65
votes
24
replies
17k
views
14 follow
Mapping Snps To Pathways
snp genotyping pathway gene enrichment
updated 7 months ago by 44k • written 14.2 years ago by 161k
4
votes
24
replies
6.1k
views
Split a concatenated alignment in multiple files
alignment fasta
updated 7 months ago by • 0 • written 9.2 years ago by ★ 2.8k
38
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 21 days ago by 19k • written 23 days ago by ▴ 580
159
votes
24
replies
63k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing splicing rna-seq
updated 11 months ago by 44k • written 11.2 years ago by 11k
48
votes
24
replies
8.3k
views
14 follow
Tool: Hera: A new tool for RNA-Seq analysis
kallisto RNA-Seq STAR gene-fusion
updated 11 months ago by 44k • written 6.8 years ago by ▴ 580
15
votes
24
replies
2.6k
views
7 follow
Forum: Airport.bio: First class ticket to any biological database in the world
RNA-Seq ChIP-Seq SNP
updated 12 months ago by 44k • written 6.1 years ago by ▴ 350
93
votes
23
replies
93k
views
15 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 4 months ago by • 0 • written 5.8 years ago by ▴ 610
34
votes
23
replies
22k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq genome
updated 8 months ago by ▴ 120 • written 6.1 years ago by ▴ 680
18
votes
23
replies
7.8k
views
7 follow
How to exclude some of breast cancer subtypes just by looking at gene expression?
RNA-Seq genome cancer gene
updated 11 months ago by • 0 • written 6.5 years ago by ▴ 970
12
votes
23
replies
8.5k
views
6 follow
motif search with ATAC-seq
motif-search ATAC-seq
updated 11 months ago by 44k • written 5.6 years ago by ★ 2.6k
6
votes
23
replies
26k
views
6 follow
devtools Installation error in R (version 3.5.3)?
github R phylogeny devtools
updated 11 months ago by 44k • written 5.1 years ago by ▴ 120
20
votes
23
replies
7.3k
views
6 follow
Tool: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
easeq Windows Visualization ChIP-Seq
updated 10 months ago by 44k • written 8.1 years ago by ▴ 460
33
votes
23
replies
4.3k
views
8 follow
Forum: Is there a file format better suited for the era of pangenomics than the .vcf? What are its attributes?
VCF file-format genomics
updated 11 months ago by 22k • written 11 months ago by 4.2k
11
votes
23
replies
1.7k
views
gatk Hardfilter Error
hardfilter
updated 11 months ago by 54k • written 11 months ago by ▴ 30
56
votes
23
replies
5.2k
views
10 follow
Tool: ASCIIGenome: Text Only Genome Viewer!
terminal genome-browser java ASCIIGenome
updated 11 months ago by 44k • written 7.9 years ago by 14k
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
10 days ago by vytarasov ▴ 180
23
votes
23
replies
10.0k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq removeBatchEffect batch-effect edger
updated 4 weeks ago by 44k • written 5.4 years ago by ▴ 130
68
votes
23
replies
50k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 9 weeks ago by • 0 • written 6.5 years ago by ★ 1.2k
31
votes
23
replies
30k
views
15 follow
Amino Acid Change To Genomic Location
snp amino-acids
updated 4 months ago by ▴ 80 • written 12.4 years ago by ▴ 110
40
votes
23
replies
4.2k
views
12 follow
Forum: Why learn programming in bioinformatics?
Programming
updated 12 months ago by 44k • written 5.7 years ago by ▴ 110
66
votes
23
replies
11k
views
9 follow
Using Hdf5 To Store Bio-Data
hdf5 storage database
updated 7 months ago by 44k • written 14.2 years ago by 161k
61
votes
23
replies
57k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 6 months ago by ★ 1.2k • written 11.2 years ago by ★ 1.3k
39
votes
23
replies
35k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 8 months ago by ▴ 40 • written 2.9 years ago by ▴ 130
6
votes
23
replies
1.6k
views
How to speed Salmon index up
metagenome genome salmon
4 months ago by young_bioinformatician ▴ 230
11
votes
22
replies
4.3k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 5 weeks ago by 44k • written 5.1 years ago by ▴ 270
3
votes
22
replies
4.1k
views
GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment
GRanges
updated 11 months ago by ★ 2.2k • written 14 months ago by • 0
31
votes
22
replies
13k
views
6 follow
Tool: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
FASTQ SeqKit FASTA
updated 11 months ago by 44k • written 7.6 years ago by 8.5k
1
vote
22
replies
2.1k
views
error with Tximport when txOut = TRUE
tximport R
updated 10 months ago by 44k • written 10 months ago by • 0
24
votes
22
replies
27k
views
11 follow
replace fasta headers with another name in a text file
perl
updated 10 months ago by • 0 • written 10.0 years ago by ▴ 60
15
votes
22
replies
8.7k
views
What Are The Most Reliable Normalization Methods For Microarrays?
microarray
updated 6 months ago by 44k • written 14.2 years ago by 3.4k
11
votes
22
replies
4.6k
views
7 follow
Which New Bioinformatics Related Tool Would You Appreciate The Most?
programming
updated 10 months ago by 44k • written 11.8 years ago by 3.2k
34
votes
22
replies
3.0k
views
11 follow
Forum: Have we failed as bioinformatician in this time of COVID-19
Bioinformatician COVID-19
updated 11 months ago by 44k • written 4.0 years ago by ▴ 10
57
votes
22
replies
29k
views
7 follow
Batch correction in DESeq2
Combat DESeq2 Batch-Effect
updated 6 weeks ago by 44k • written 4.6 years ago by ▴ 510
30
votes
22
replies
58k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r genomics entrez
updated 10 months ago by • 0 • written 11.1 years ago by ▴ 100
138
votes
22
replies
66k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 11 months ago by 88k • written 6.5 years ago by ★ 1.9k
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 4 weeks ago by 44k • written 6.9 years ago by ★ 1.3k
5
votes
22
replies
12k
views
sra toolkit program fastq-dump question.
sratoolkit fastq-dump
updated 10 months ago by 44k • written 9.3 years ago by ▴ 10
12
votes
22
replies
2.0k
views
Can anyone simplify GATK installation
GATK
4 months ago by Tundup • 0
14
votes
21
replies
10k
views
7 follow
HOMER annotatePeaks.pl problem
RNA-Seq ChIP-Seq HOMER
updated 11 months ago by 44k • written 6.7 years ago by ▴ 110
15
votes
21
replies
5.7k
views
7 follow
alphafold online availability and use case
alphafold structure prediction
written 2.8 years ago by ▴ 70
23
votes
21
replies
9.1k
views
9 follow
fastest UMAP method
UMAP R
updated 6 months ago by ★ 27k • written 4.6 years ago by ▴ 30
60
votes
21
replies
3.9k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome assembly
updated 8 months ago by 54k • written 8 months ago by ▴ 60
27
votes
21
replies
38k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 7 months ago by ▴ 70 • written 9.9 years ago by ▴ 170
18
votes
21
replies
4.5k
views
Tool: uQ - small binary FASTQ
Compression FASTQ
updated 10 months ago by 44k • written 7.2 years ago by 13k
38
votes
21
replies
19k
views
8 follow
Tool: pybam - 100% python BAM reader
python htspython bam pysam
updated 11 months ago by 44k • written 8.1 years ago by 13k
10
votes
21
replies
3.4k
views
How to interpret heatmap using plotheatmap from deeptools?
ATAC-seq deeptools
9 months ago by Chris ▴ 280
12,517 results • Page 3 of 251
Recent Votes
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
Comment: Practical Haplotype Graph v2 not finding correct paths
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Recent Replies
Answer: Question about samtools view flags (paired reads vs. properly paired reads) by Pierre Lindenbaum 161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set by Matthias Zepper 4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R by bk11 ★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w by Pierre Lindenbaum 161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set by bk11 ★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB by DBScan ▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths by beantkapoor16 ▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results by Bjorn • 0
Thank you!
Comment: Generating a Bed file from a Fasta file by Pierre Lindenbaum 161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths by beantkapoor16 ▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file by pirku • 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice by GenoMax 142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file by Pierre Lindenbaum 161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line by Arthur • 0
If it cans help, I got the same error message : There were errors in the input file (listed above). According to "mainparams" the inp…
Comment: CreateSeuratObject taking very long by Nitin Narwade ★ 1.6k
I am not sure whether it will speedup the conversion but you can give it a try. convert your dataframe into a sparse matrix before creatin…
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