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12,723 results • Page 5 of 255
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30
votes
12
replies
3.9k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 4 weeks ago by 43k • written 4.1 years ago by ▴ 330
30
votes
16
replies
2.3k
views
9 follow
Forum: Which programming langauge shall I start as a beginner in Bioinformatics
programming-language single-cell
updated 11 months ago by 43k • written 4.1 years ago by • 0
30
votes
15
replies
10k
views
7 follow
Tool: Snakemake--Python-Based Workflow Management
workflow snakemake python
updated 10 months ago by 43k • written 10.5 years ago by 26k
30
votes
13
replies
11k
views
Web Tool That Converts A Pubmed Query Into A Wordle Of The Abstracts
pubmed
updated 10 months ago by 43k • written 13.7 years ago by 4.9k
29
votes
12
replies
13k
views
10 follow
What Is The Best Place In The World To Do Bioinformatics?
education subjective
updated 7 months ago by 43k • written 14.2 years ago by ▴ 650
29
votes
20
replies
3.8k
views
Tool: FastQt : a clone of FastQC in C++/Qt
fastqc Cpp fastq Qt
updated 10 months ago by 43k • written 7.4 years ago by ★ 2.4k
29
votes
18
replies
3.3k
views
7 follow
Forum: Should I quit PhD program?
education career research phd
updated 12 months ago by 43k • written 6.0 years ago by ▴ 30
29
votes
18
replies
2.7k
views
12 follow
Forum: what are the big questions in bioinformatics field nowadays
genome
updated 11 months ago by 43k • written 4.2 years ago by ▴ 20
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 15 days ago by • 0 • written 12.8 years ago by ★ 1.7k
29
votes
5
replies
3.5k
views
How Important Is It To Belong To A Professional Society In Computational Biology?
career subjective
updated 6 months ago by 43k • written 14.2 years ago by ▴ 650
29
votes
13
replies
8.5k
views
7 follow
Tools For Visualizing Significantly Altered Pathways And Related Genes In A Pathway Graph ?
pathway-visualization
updated 10 months ago by 43k • written 13.4 years ago by ★ 1.3k
29
votes
11
replies
8.8k
views
An Interactive Heatmap For Viewing Expression Data Matrices
heatmap microarray visualization
updated 10 months ago by 43k • written 13.7 years ago by 1.9k
28
votes
13
replies
14k
views
Taxonomy Of Blast Hits
blast taxonomy
updated 7 months ago by 43k • written 14.2 years ago by 4.6k
28
votes
16
replies
31k
views
11 follow
How Do I Convert From Bed Format To Gff Format?
gff galaxy bed
updated 7 months ago by 43k • written 14.6 years ago by 100k
28
votes
27
replies
15k
views
9 follow
Extracting A Subset Of Sequences From A Fastq File (Biopython Speed)
biopython python fastq next-gen-sequencing
updated 6 months ago by 43k • written 14.1 years ago by 4.6k
28
votes
11
replies
19k
views
9 follow
Salary For A Bioinformatics Programmer In Europe?
career
updated 12 months ago by 43k • written 12.7 years ago by 2.3k
28
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 ▴ 90
28
votes
7
replies
11k
views
Tool: Quast Is A Convenient Tool For Assembly Evaluation
assembly quality
updated 10 months ago by 43k • written 11.2 years ago by ★ 1.3k
28
votes
20
replies
21k
views
7 follow
how do I run repeat masker
repeatmasker
updated 4 months ago by 11k • written 8.4 years ago by ▴ 80
28
votes
14
replies
11k
views
7 follow
Compare Two Protein Sequences Using Local Blast
biopython blast
updated 6 months ago by 43k • written 14.2 years ago by ▴ 120
28
votes
15
replies
2.3k
views
12 follow
Forum: Should bioinformaticians learn the scientific names of plants and animals?
sequence
updated 11 months ago by 43k • written 5.9 years ago by ▴ 10
28
votes
17
replies
5.1k
views
7 follow
Tool: PCAtools: everything Principal Components Analysis
eigenvector pca bioconductor R
updated 11 months ago by 43k • written 5.3 years ago by 88k
28
votes
11
replies
34k
views
10 follow
Samtools View: Only Forward Or Reverse Strand
samtools strand
updated 3 months ago by • 0 • written 12.5 years ago by ▴ 540
28
votes
19
replies
15k
views
10 follow
How To Generate Mutations In Sequences Of A Fasta File?
fasta python mutation sequence
updated 10 months ago by 43k • written 12.7 years ago by ★ 1.5k
28
votes
7
replies
19k
views
6 follow
VCF merge or concatenate?
snp VCF VCFTools
written 4.8 years ago by ▴ 60
28
votes
16
replies
9.3k
views
7 follow
What Does Bwa'S '-N' Parameter Mean?
bwa
updated 9 months ago by ▴ 20 • written 12.3 years ago by ★ 1.8k
28
votes
4
replies
15k
views
Tool: Plotting GSEA output in R
RNA-Seq javaGSEA GSEA
updated 11 months ago by 43k • written 7.8 years ago by ▴ 850
28
votes
13
replies
15k
views
7 follow
Create Consensus Sequences For Sequence Pairs Within A Multiple Alignment?
consensus phylogenetics fasta multiple-alignment
updated 6 months ago by 43k • written 14.1 years ago by ★ 2.0k
27
votes
17
replies
22k
views
8 follow
BioPython: convert fasta to fastq without quality score input file
parsing phred fasta BioPython fastq
updated 11 months ago by • 0 • written 10.0 years ago by 5.8k
27
votes
6
replies
16k
views
Tool: Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 10 months ago by 43k • written 11.9 years ago by 100k
27
votes
8
replies
11k
views
7 follow
Any Quick Sort Method For Large Bed File As 20G In Size?
sort bed
updated 3 months ago by ▴ 530 • written 11.2 years ago by ▴ 310
27
votes
13
replies
6.0k
views
Tool: DEA.R: Command line script for differential expression analysis with R packages (DESeq2/edgeR/limma-voom)
edgeR DESeq2 limma RNA-Seq
updated 10 months ago by 43k • written 7.8 years ago by 47k
27
votes
24
replies
2.5k
views
7 follow
Code Golf - bisulfite conversion
bisulfite bsseq code-golf
updated 11 months ago by 43k • written 5.6 years ago by 22k
27
votes
4
replies
2.7k
views
How Should A Departing Programmer Organize Things For Successors?
software
updated 6 months ago by 43k • written 14.1 years ago by ▴ 330
27
votes
10
replies
4.5k
views
7 follow
Which Are All The Databases For Annotations Of Biological Pathways?
pathway database annotation
updated 6 months ago by 43k • written 14.1 years ago by 28k
27
votes
27
replies
10k
views
6 follow
How To Detect And Query Poly-Allelic Snps?
snp allele biomart dbsnp
updated 6 months ago by 43k • written 14.2 years ago by 54k
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
26
votes
4
replies
5.3k
views
Tool: Dgidb - Mining The Druggable Genome
dgidb drug-gene-interaction
updated 10 months ago by 43k • written 10.6 years ago by 20k
26
votes
50
replies
14k
views
8 follow
Tool: Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta multi-fasta illumina
updated 10 months ago by 43k • written 8.0 years ago by ▴ 50
26
votes
22
replies
14k
views
10 follow
Tool: BBSketch - A Tool for Rapid Sequence Comparison
minhash sketch bbmap blast
updated 12 months ago by 43k • written 7.3 years ago by 20k
26
votes
9
replies
10k
views
6 follow
DESeq2 modelling and Wald's test
RNA-Seq DESeq2
updated 11 months ago by ▴ 640 • written 6.1 years ago by ▴ 150
26
votes
5
replies
24k
views
BLAST options: max_target_seqs and num_alignments
blast
updated 8 weeks ago by ▴ 30 • written 9.5 years ago by ★ 1.4k
26
votes
16
replies
6.7k
views
Which Human Tumor Cell Line/Sample Genomes Have Been Already Sequenced Completely?
genome next-gen-sequencing
updated 6 months ago by 43k • written 14.2 years ago by 4.3k
26
votes
8
replies
1.7k
views
7 follow
Forum: Reasons to refuse to give support
design rna-seq statistics
updated 11 months ago by 43k • written 5.5 years ago by 8.3k
26
votes
9
replies
8.4k
views
Provide A Book Review For "Bioinformatics Programming Using Python" By Mitchell L. Model
python books
updated 7 months ago by 43k • written 14.2 years ago by 2.3k
26
votes
27
replies
2.2k
views
10 follow
Forum: Determining computer time required
computer hpc time
updated 4 months ago by ★ 6.0k • written 4 months ago by ▴ 40
26
votes
9
replies
19k
views
8 follow
Favorite Splice Site Prediction/Evaluation Tools
splicing prediction
updated 11 months ago by ▴ 30 • written 11.5 years ago by 3.5k
26
votes
11
replies
5.1k
views
7 follow
How To Filter Affymetrix Probes Related To Murine Genes Encoding Membran Proteins
affymetrix gene annotation mouse gene
updated 6 months ago by 43k • written 14.1 years ago by 4.3k
26
votes
18
replies
8.6k
views
10 follow
Indexing Compressed Fastq-Like Data
fastq
updated 10 months ago by 43k • written 13.8 years ago by ★ 5.1k
25
votes
19
replies
8.2k
views
10 follow
Tool: pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork R pathway-enrichment
updated 11 months ago by 43k • written 6.2 years ago by ★ 1.3k
12,723 results • Page 5 of 255
Recent Votes
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
Differentially expressed genes between Seurat objects
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Recent Replies
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Details on salmon index by Rob 6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Comment: Help! Reconstruction of locus, order contigs by BATMAN • 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint yes but for example for the kallisto results I have expression for 2080 genes (transcripts) and the rest are 0 but in my STAR resu…
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