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117,001 results • Page 5 of 2341
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Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
r books bioconductor
updated 6 months ago by 43k • written 14.1 years ago by 54k
30
votes
34
replies
6.8k
views
enrichment of gene set with enrichR
enrichR RNA-Seq R
updated 6.2 years ago by 47k • written 6.2 years ago by ▴ 30
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 11.1 years ago by 6.1k
54
votes
34
replies
5.0k
views
13 follow
Forum: Should We Release Database Dumps Of All Questions On Biostar?
meta biostars
updated 15 months ago by 43k • written 13.5 years ago by 100k
80
votes
34
replies
5.4k
views
11 follow
Forum: Authorship issues- how to resolve?
authorship
updated 16 months ago by 43k • written 9.0 years ago by ▴ 520
2
votes
34
replies
6.8k
views
How to install pip on HPC server
software error
6.3 years ago by Bioinfonext ▴ 460
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
19
votes
34
replies
5.8k
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 9.5 years ago by ▴ 150
12
votes
34
replies
5.2k
views
Hidden Markov Models Within Sequence Analysis -- Dispelling Misconceptions + Fixing Explanations
sequencing
updated 12.2 years ago by ★ 1.3k • written 12.6 years ago by ▴ 200
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
16k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq demultiplexing
updated 10 weeks ago by ★ 2.2k • written 6.8 years ago by ▴ 350
65
votes
34
replies
27k
views
20 follow
Phylogenetic Analysis Of Whole Genomes
phylogenetics tree
updated 2.2 years ago by 43k • written 13.8 years ago by ▴ 130
41
votes
34
replies
17k
views
10 follow
Best tool for variant calling
SNP genome alignment next-gen
updated 5.5 years ago by • 0 • written 6.0 years ago by ▴ 520
16
votes
34
replies
4.9k
views
7 follow
GC percent detection for several number of genes
GC% large number of genes
7.1 years ago by nazaninhoseinkhan ▴ 520
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 2.1 years ago by 43k • written 9.3 years ago by ▴ 920
103
votes
34
replies
114k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 4 months ago by 43k • written 12.0 years ago by ▴ 390
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
70
votes
33
replies
18k
views
18 follow
Choosing Random Set Of Seqs From Larger Set
random fasta
updated 2.0 years ago by 43k • written 12.2 years ago by ▴ 190
50
votes
33
replies
56k
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 88k • written 7.8 years ago by ▴ 340
27
votes
33
replies
17k
views
high % of reads mapped to multiple loci after STAR mapping
RNA-Seq STAR single-end
updated 6.5 years ago by ▴ 990 • written 6.5 years ago by ★ 1.2k
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 12.6 years ago by 54k • written 12.6 years ago by ▴ 350
121
votes
33
replies
39k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 12 months ago by ★ 2.5k • written 10.7 years ago by 11k
10
votes
33
replies
3.9k
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
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 13.5 years ago by 18k • written 13.5 years ago by 28k
27
votes
33
replies
3.8k
views
7 follow
Forum: Biostars question catagories
statistics biostars meta
updated 13 months ago by 43k • written 7.6 years ago by 13k
143
votes
33
replies
30k
views
20 follow
C/C++ Libraries For Bioinformatics?
c c
updated 5.1 years ago by ▴ 50 • written 13.9 years ago by 13k
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
16
votes
33
replies
8.5k
views
9 follow
Back-filling missing genotypes in merged VCF
vcf
updated 17 months ago by 161k • written 9.5 years ago by ★ 1.1k
41
votes
33
replies
18k
views
10 follow
How To Convert Xml Into A Decent Parseable Format?
xml parsing perl subjective
updated 13.0 years ago by ▴ 30 • written 13.0 years ago by ★ 2.3k
29
votes
33
replies
8.3k
views
12 follow
getBM error while using bioMart
biomart getBM ensembl
updated 3.6 years ago by • 0 • written 3.6 years ago by ▴ 160
6
votes
33
replies
2.8k
views
I need to understand this image
phylogenies
updated 7.3 years ago by 23k • written 7.3 years ago by • 0
11
votes
33
replies
17k
views
How we can analyze sanger sequence chromatogram?
SNP sequencing alignment sanger
updated 2.3 years ago by 43k • written 9.5 years ago by ▴ 40
298
votes
33
replies
109k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 14 months ago by 43k • written 10.6 years ago by 20k
141
votes
33
replies
67k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 18 months ago by 43k • written 10.1 years ago by ▴ 510
93
votes
32
replies
33k
views
26 follow
Linux Distros Best Suited For Bioinformatics?
linux
written 12.3 years ago by ▴ 150
3
votes
32
replies
3.5k
views
fastqc report for degradome reads
fastqc adaptor
6.1 years ago by Sam ▴ 150
32
votes
32
replies
8.1k
views
11 follow
Should We Be Using Much More Json In Our Delimited Data Formats?
gff vcf
updated 13.3 years ago by ★ 2.4k • written 13.3 years ago by ★ 3.3k
88
votes
32
replies
9.7k
views
11 follow
Forum: Vintage / unconventional pictures for Bioinformatics
history picture
updated 2.2 years ago by 43k • written 9.6 years ago by 161k
53
votes
32
replies
13k
views
13 follow
Bio-Javascript?
updated 2.1 years ago by 43k • written 13.2 years ago by ★ 3.1k
82
votes
32
replies
7.8k
views
13 follow
Forum: Shall We Go Back To Stackexchange?
meta
updated 14 months ago by 43k • written 11.5 years ago by ★ 3.6k
10
votes
32
replies
3.8k
views
6 follow
Why my CD31+ endothelial cells RNAseq didn't express CD31?
CD31 HISAT2 endothelialcells Stringtie RNAseq
3.1 years ago by Youyy • 0
9
votes
32
replies
3.0k
views
Differentially gene expressed analyses of two different samples
RNA-Seq R next-gen rna-seq
updated 7.5 years ago by ▴ 610 • written 7.5 years ago by ▴ 820
129
votes
32
replies
130k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 2.1 years ago by 43k • written 13.2 years ago by ▴ 540
153
votes
32
replies
8.6k
views
23 follow
Picking A Programming Language And Where To Begin
programming next-gen sequencing c subjective
updated 12.3 years ago by ▴ 60 • written 12.8 years ago by ★ 2.8k
0
votes
32
replies
9.6k
views
DoHeatmap clusters, Seurat pipeline
scRNA-sequencing
3.6 years ago by Morris_Chair ▴ 360
9
votes
31
replies
5.0k
views
6 follow
Clustering Million Points : Transcript Start And End Sites
clustering
updated 12.1 years ago by 18k • written 12.1 years ago by ★ 1.6k
6
votes
31
replies
9.9k
views
16 follow
Cnv Calling Methods For The Illumina Omni2.5 - Penncnv And Quantisnp Possible?
cnv illumina copynumber
updated 10.8 years ago by • 0 • written 12.7 years ago by ★ 3.4k
17
votes
31
replies
5.8k
views
Finding the best model for expression data (RNA-Seq counts)
RNA-Seq glm model fit regression
updated 5.2 years ago by 19k • written 5.2 years ago by ▴ 250
13
votes
31
replies
3.9k
views
Feature extraction from DNA sequence
snp machine learning deep learning
updated 5.2 years ago by ▴ 180 • written 5.5 years ago by ▴ 150
89
votes
31
replies
14k
views
23 follow
Best Graphics Gallery Or Blogs For Bioinformatics Use
graphs visualization genomics
updated 21 months ago by 43k • written 12.2 years ago by ★ 1.5k
117,001 results • Page 5 of 2341
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C: How can I perform Differential expression analysis with just one control and one
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Comment: scRNAseq Differential expression analysis
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Recent Replies
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
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.
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