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1,000 results • Page 5 of 20
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31
votes
34
replies
7.4k
views
11 follow
Forum: pros- and cons- : programming skills vs. GUI
programming lecture
updated 13 months ago by 43k • written 8.4 years ago by ★ 4.7k
12
votes
34
replies
5.1k
views
Hidden Markov Models Within Sequence Analysis -- Dispelling Misconceptions + Fixing Explanations
sequencing
updated 12.1 years ago by ★ 1.3k • written 12.6 years ago by ▴ 200
54
votes
34
replies
4.9k
views
13 follow
Forum: Should We Release Database Dumps Of All Questions On Biostar?
meta biostars
updated 14 months ago by 43k • written 13.4 years ago by 100k
2
votes
34
replies
6.8k
views
How to install pip on HPC server
software error
6.2 years ago by Bioinfonext ▴ 460
19
votes
34
replies
5.7k
views
6 follow
How can I convert the blast results into a matrix?
perl linux python blast
updated 2.2 years ago by 43k • written 9.4 years ago by ▴ 150
44
votes
34
replies
13k
views
7 follow
Technical replicates in RNAseq
RNA-Seq technical_replicates
2.2 years ago by grant.hovhannisyan ★ 2.6k
16
votes
34
replies
4.8k
views
7 follow
GC percent detection for several number of genes
GC% large number of genes
7.1 years ago by nazaninhoseinkhan ▴ 520
41
votes
34
replies
16k
views
10 follow
Best tool for variant calling
SNP genome alignment next-gen
updated 5.4 years ago by • 0 • written 5.9 years ago by ▴ 510
147
votes
34
replies
55k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 14 months ago by 43k • written 11.0 years ago by 6.0k
16
votes
34
replies
12k
views
6 follow
Why am I unable to load my data from a tab separated file into R?
microarray programming R
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 920
30
votes
34
replies
6.7k
views
enrichment of gene set with enrichR
enrichR RNA-Seq R
updated 6.1 years ago by 47k • written 6.1 years ago by ▴ 30
172
votes
34
replies
26k
views
29 follow
Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
r books bioconductor
updated 5 months ago by 43k • written 14.1 years ago by 54k
11
votes
34
replies
2.2k
views
De novo transcriptome from PE reads with high multi-mapping rate (Bowtie2)
RNA-Seq read support Assembly bowtie2
3.6 years ago by Dunois ★ 2.5k
15
votes
34
replies
12k
views
Improving efficiency of awk for large files
awk
updated 18 months ago by 43k • written 8.8 years ago by ▴ 350
65
votes
34
replies
27k
views
20 follow
Phylogenetic Analysis Of Whole Genomes
phylogenetics tree
updated 2.1 years ago by 43k • written 13.8 years ago by ▴ 130
15
votes
34
replies
16k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq demultiplexing
updated 7 weeks ago by ★ 2.1k • written 6.7 years ago by ▴ 350
50
votes
33
replies
55k
views
10 follow
I would like to add gene names to a volcano plot obtained from DEseq2
RNA-Seq DEseq2 R
updated 6.0 years ago by 87k • written 7.8 years ago by ▴ 340
11
votes
33
replies
17k
views
How we can analyze sanger sequence chromatogram?
SNP sequencing alignment sanger
updated 2.2 years ago by 43k • written 9.5 years ago by ▴ 40
138
votes
33
replies
66k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 18 months ago by 43k • written 10.0 years ago by ▴ 490
70
votes
33
replies
17k
views
18 follow
Choosing Random Set Of Seqs From Larger Set
random fasta
updated 24 months ago by 43k • written 12.1 years ago by ▴ 190
29
votes
33
replies
8.1k
views
12 follow
getBM error while using bioMart
biomart getBM ensembl
updated 3.5 years ago by • 0 • written 3.6 years ago by ▴ 160
298
votes
33
replies
108k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 14 months ago by 43k • written 10.5 years ago by 20k
12
votes
33
replies
3.2k
views
Missing sequences in local NT database
nt blast ncbi blastdbcmd
updated 5.6 years ago by 15k • written 5.6 years ago by ★ 2.7k
24
votes
33
replies
8.5k
views
Contribute To The Nat Gen Paper "Principles For The Post-Gwas Functional Characterisation Of Risk Loci"
gwas snp
updated 13.4 years ago by 18k • written 13.4 years ago by 28k
121
votes
33
replies
39k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 11 months ago by ★ 2.5k • written 10.7 years ago by 11k
27
votes
33
replies
3.8k
views
7 follow
Forum: Biostars question catagories
statistics biostars meta
updated 12 months ago by 43k • written 7.5 years ago by 13k
11
votes
33
replies
4.0k
views
Detect Regions In A List That Are Within 1 Megabase Of Each Other
python snp genomics overlap
updated 12.5 years ago by 54k • written 12.5 years ago by ▴ 350
41
votes
33
replies
18k
views
10 follow
How To Convert Xml Into A Decent Parseable Format?
xml parsing perl subjective
updated 12.9 years ago by ▴ 30 • written 12.9 years ago by ★ 2.3k
48
votes
33
replies
43k
views
16 follow
Extract A Group Of Fasta Sequences From A File
fasta python perl biopython bioperl
updated 2.4 years ago by 43k • written 13.8 years ago by ▴ 60
10
votes
33
replies
3.8k
views
Looking for a tool like fastq screen but for ONT data
gridion nanopore ont minion
updated 10 months ago by 43k • written 5.8 years ago by ★ 1.4k
27
votes
33
replies
17k
views
high % of reads mapped to multiple loci after STAR mapping
RNA-Seq STAR single-end
updated 6.4 years ago by ▴ 990 • written 6.4 years ago by ★ 1.2k
6
votes
33
replies
2.8k
views
I need to understand this image
phylogenies
updated 7.2 years ago by 23k • written 7.2 years ago by • 0
143
votes
33
replies
30k
views
20 follow
C/C++ Libraries For Bioinformatics?
c c
updated 5.0 years ago by ▴ 50 • written 13.9 years ago by 13k
16
votes
33
replies
8.4k
views
9 follow
Back-filling missing genotypes in merged VCF
vcf
updated 16 months ago by 161k • written 9.5 years ago by ★ 1.1k
10
votes
32
replies
3.7k
views
6 follow
Why my CD31+ endothelial cells RNAseq didn't express CD31?
CD31 HISAT2 endothelialcells Stringtie RNAseq
3.0 years ago by Youyy • 0
0
votes
32
replies
9.4k
views
DoHeatmap clusters, Seurat pipeline
scRNA-sequencing
3.6 years ago by Morris_Chair ▴ 350
93
votes
32
replies
33k
views
26 follow
Linux Distros Best Suited For Bioinformatics?
linux
written 12.2 years ago by ▴ 150
88
votes
32
replies
9.6k
views
11 follow
Forum: Vintage / unconventional pictures for Bioinformatics
history picture
updated 2.1 years ago by 43k • written 9.5 years ago by 161k
3
votes
32
replies
3.4k
views
fastqc report for degradome reads
fastqc adaptor
6.1 years ago by Sam ▴ 150
153
votes
32
replies
8.5k
views
23 follow
Picking A Programming Language And Where To Begin
programming next-gen sequencing c subjective
updated 12.2 years ago by ▴ 60 • written 12.7 years ago by ★ 2.8k
32
votes
32
replies
8.0k
views
11 follow
Should We Be Using Much More Json In Our Delimited Data Formats?
gff vcf
updated 13.2 years ago by ★ 2.4k • written 13.2 years ago by ★ 3.3k
82
votes
32
replies
7.7k
views
13 follow
Forum: Shall We Go Back To Stackexchange?
meta
updated 14 months ago by 43k • written 11.4 years ago by ★ 3.6k
9
votes
32
replies
3.0k
views
Differentially gene expressed analyses of two different samples
RNA-Seq R next-gen rna-seq
updated 7.4 years ago by ▴ 610 • written 7.4 years ago by ▴ 820
129
votes
32
replies
129k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 2.1 years ago by 43k • written 13.1 years ago by ▴ 540
53
votes
32
replies
13k
views
13 follow
Bio-Javascript?
updated 2.0 years ago by 43k • written 13.2 years ago by ★ 3.1k
9
votes
31
replies
4.9k
views
6 follow
Clustering Million Points : Transcript Start And End Sites
clustering
updated 12.0 years ago by 18k • written 12.1 years ago by ★ 1.6k
59
votes
31
replies
4.9k
views
12 follow
News: Example of how bioinformaticians can publish in Scientific Reports (by nature publishing group) using publicly available NGS data
publication NGS
updated 12 months ago by 43k • written 7.3 years ago by 11k
31
votes
31
replies
2.1k
views
collecting ultraconserved elements from RNA-seq data
RNA-Seq sequence genome
updated 7.7 years ago by ★ 1.7k • written 7.7 years ago by ★ 3.4k
38
votes
31
replies
2.8k
views
10 follow
Forum: To the Biologists out there: What bioinf tool are you missing?
education career
updated 12 months ago by 43k • written 7.8 years ago by ▴ 180
17
votes
31
replies
5.7k
views
Finding the best model for expression data (RNA-Seq counts)
RNA-Seq glm model fit regression
updated 5.1 years ago by 19k • written 5.1 years ago by ▴ 250
1,000 results • Page 5 of 20
Recent Votes
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A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
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Scholar to Alex Reynolds 35k
Popular Question to chaco001 ▴ 40
Commentator to GenoMax 141k
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Recent Replies
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by Mensur Dlakic ★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq by dsull ★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708) by Gordon Smyth ★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR? by Gordon Smyth ★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu by Gordon Smyth ★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing by cao510927 ▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Alex Reynolds 35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data by bk11 ★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq by GenoMax 141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq by dsull ★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i by ATpoint 82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by BioinfGuru ★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
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