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13,335 results • Page 3 of 267
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56
votes
52
replies
49k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 10 months ago by 43k • written 9.7 years ago by 7.5k
56
votes
19
replies
4.0k
views
9 follow
Forum: How to apply for a job
resume cover-letter application CV
updated 11 months ago by 43k • written 6.7 years ago by 23k
56
votes
23
replies
5.0k
views
10 follow
Tool: ASCIIGenome: Text Only Genome Viewer!
terminal genome-browser java ASCIIGenome
updated 9 months ago by 43k • written 7.8 years ago by 14k
54
votes
7
replies
4.0k
views
6 follow
Tool: Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinformatics
genome-viewer
updated 9 months ago by 43k • written 10.9 years ago by ▴ 40
54
votes
10
replies
21k
views
10 follow
Finding Common Motifs In Sequences
motif
updated 6 months ago by 43k • written 14.6 years ago by ▴ 130
54
votes
13
replies
10k
views
6 follow
Tool: Bedtools: Analyzing Genomic Features
bedtools
updated 9 months ago by 43k • written 12.0 years ago by 100k
54
votes
17
replies
5.8k
views
8 follow
Is annotation of enhancers to nearest gene pointless?
enhancer annotation
updated 11 months ago by 43k • written 6.9 years ago by ★ 1.7k
53
votes
13
replies
7.8k
views
9 follow
Has Enhancer And Transcription Factor Binding Site Prediction Already Been Made Redundant?
transcription-factor-binding-site
updated 5 months ago by 43k • written 14.1 years ago by ★ 1.3k
53
votes
11
replies
28k
views
10 follow
Out Of Disk Space With Picard Tools ?
picard
updated 9 months ago by 43k • written 12.0 years ago by ★ 2.9k
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing fastq
updated 5 months ago by 161k • written 14.0 years ago by ▴ 660
52
votes
15
replies
30k
views
10 follow
Where To Download Pam50 Gene Set?
cancer annotation classification
updated 9 months ago by ★ 4.3k • written 10.7 years ago by ▴ 940
52
votes
8
replies
20k
views
6 follow
Fast Interval Intersection Methodologies
genomics
updated 6 months ago by 43k • written 14.1 years ago by ★ 1.0k
52
votes
21
replies
49k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 9 months ago by 43k • written 12.0 years ago by ★ 1.5k
52
votes
8
replies
59k
views
7 follow
Subsampling Bam File With Samtools
bam samtools
updated 3 months ago by ▴ 10 • written 10.8 years ago by ▴ 250
51
votes
6
replies
18k
views
Decoy In Reference Assembly
1000genomes
updated 11 months ago by • 0 • written 10.9 years ago by ▴ 420
51
votes
25
replies
6.8k
views
10 follow
What Is Your Experience With Bioinformatics Webservices?
web-service subjective
updated 5 months ago by 43k • written 14.1 years ago by 54k
50
votes
13
replies
56k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 6 months ago by ▴ 160 • written 8.3 years ago by ▴ 490
50
votes
16
replies
14k
views
12 follow
Tool: Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr software ngs
updated 10 months ago by 43k • written 10.6 years ago by ▴ 450
50
votes
18
replies
36k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq macs ChIP-Seq peaks
updated 9 months ago by 43k • written 7.6 years ago by 13k
49
votes
18
replies
15k
views
12 follow
What Phylogeny Viewing Software Do You Use?
software phylogenetics visualization
updated 5 months ago by 43k • written 14.1 years ago by ▴ 390
49
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 19 days ago by 100k • written 8.1 years ago by 43k
49
votes
20
replies
2.0k
views
10 follow
Forum: First experiences matter
first-time tolerance
updated 3 months ago by ★ 2.6k • written 3 months ago by ★ 27k
48
votes
18
replies
32k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter sequence human genome
updated 5 months ago by 43k • written 14.0 years ago by ★ 1.7k
48
votes
14
replies
26k
views
8 follow
Gene Network Construction... Web Based Tool
gene-network
updated 9 months ago by 43k • written 12.9 years ago by ★ 2.8k
48
votes
16
replies
5.4k
views
12 follow
Bio-Informatics Results Supporting Ongoing Evolution
evolution publication
written 13.3 years ago by ▴ 310
48
votes
9
replies
43k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 11 weeks ago by ▴ 640 • written 7.5 years ago by ▴ 550
48
votes
24
replies
8.2k
views
14 follow
Tool: Hera: A new tool for RNA-Seq analysis
kallisto RNA-Seq STAR gene-fusion
updated 9 months ago by 43k • written 6.7 years ago by ▴ 580
48
votes
8
replies
6.7k
views
8 follow
How Far Does Bioinformatics Go?
meta subjective
updated 6 months ago by 43k • written 14.1 years ago by 5.4k
48
votes
21
replies
5.1k
views
9 follow
What Online Gene-Centric Resources Do You Use?
gene database
updated 5 months ago by 43k • written 14.0 years ago by 4.9k
47
votes
15
replies
16k
views
10 follow
DESeq2 compare all levels
differential-gene-expression RNA-Seq DESeq2
updated 28 days ago by • 0 • written 5.8 years ago by ★ 1.6k
47
votes
26
replies
4.0k
views
11 follow
Blog: Evolution of Biostars
meta Biostars
updated 7 months ago by ▴ 70 • written 5.1 years ago by 7.1k
47
votes
30
replies
4.3k
views
10 follow
Forum: Bioinformatics software distribution
software
updated 11 months ago by 43k • written 7.1 years ago by ★ 2.7k
46
votes
18
replies
9.9k
views
8 follow
Tips To Build A Data Storage For Bioinformatics
data
updated 5 months ago by 43k • written 14.1 years ago by 3.4k
46
votes
13
replies
14k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 5 weeks ago by • 0 • written 3.5 years ago by 3.2k
46
votes
14
replies
27k
views
12 follow
Which Bioinformatics Tools Are Written In Python
python
updated 10 months ago by 43k • written 11.7 years ago by ★ 1.1k
46
votes
16
replies
5.9k
views
12 follow
News: Google announces DeepVariant
genome deep-learning google
updated 11 months ago by 43k • written 6.4 years ago by ▴ 990
45
votes
19
replies
2.8k
views
9 follow
Forum: Where and how NGS techniques are heading for the next 5 years?
next-gen NGS
updated 11 months ago by 43k • written 6.8 years ago by 5.8k
45
votes
9
replies
58k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen RNA-Seq single-cell R
updated 8 months ago by ▴ 160 • written 4.4 years ago by ▴ 160
44
votes
9
replies
5.4k
views
6 follow
How Much Do You Trust Geneontology Annotations?
gene-function subjective
updated 6 months ago by 43k • written 14.2 years ago by 28k
44
votes
4
replies
20k
views
Best way to compare two samples in a VCF file
VCF Variant Genotype Comparison SNP
updated 8 months ago by 43k • written 7.4 years ago by ★ 3.6k
43
votes
21
replies
5.4k
views
9 follow
Helping Biostar Grow
biostars
updated 5 months ago by 43k • written 14.0 years ago by 11k
43
votes
37
replies
2.5k
views
7 follow
Forum: Checking the quality and reliability in bioinformatics
reproducibility
updated 11 months ago by 43k • written 6.5 years ago by ★ 4.3k
43
votes
44
replies
5.6k
views
14 follow
Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?
metagenomics amplicon macbook Intel MacOs
updated 6 months ago by ★ 3.5k • written 6 months ago by ▴ 10
43
votes
28
replies
5.6k
views
13 follow
Post Your Prefered Bioinformatics Short Code
code
updated 5 months ago by 43k • written 14.0 years ago by 11k
43
votes
12
replies
5.8k
views
11 follow
What Is The Best Way To Share Scripts Between Members Of A Lab?
general subjective
updated 6 months ago by 43k • written 14.1 years ago by 28k
42
votes
15
replies
12k
views
12 follow
Preferred Tools For Making Analysis Pipeline Flowchart ?
pipeline
updated 9 months ago by 43k • written 11.2 years ago by ▴ 730
42
votes
16
replies
33k
views
14 follow
Generating consensus sequence from bam file
genome samtools bwa fasta
updated 6 months ago by ★ 1.2k • written 5.1 years ago by ▴ 70
41
votes
27
replies
5.9k
views
8 follow
Forum: Why bioinformaticians need to know programming languages?
Python R Programming
updated 11 months ago by 43k • written 6.9 years ago by ▴ 90
41
votes
13
replies
26k
views
13 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq DESeq2 geneontology GSEA
updated 5 weeks ago by ▴ 110 • written 6.5 years ago by ▴ 290
40
votes
35
replies
13k
views
10 follow
find positions of a short sequence in a genome
sequence search
updated 8 months ago by ★ 1.5k • written 7.6 years ago by 13k
13,335 results • Page 3 of 267
Recent Votes
Comment: Integration of transcriptomics and proteomics: difficult matching names
Comment: Integration of transcriptomics and proteomics: difficult matching names
A: How to filter mutant allele frequency in Variant Effect Predictor (VEP)?
Answer: Rename multiple fastq.gz files
Comment: VCF to human friendly form?
Comment: Integration of transcriptomics and proteomics: difficult matchin names
BRAKER3 genome annotation
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Recent Replies
Comment: GSEA analysis in R by sansan_96 ▴ 80
One example: ``` ### ego3 <- gseGO(geneList = geneList, OrgDb = org.Hs.eg.db, ont = "CC", …
Comment: How to filter columns in a raw sparse matrix in R by bk11 ★ 2.3k
You can do this- good_cells <-c(all_good_cells_rhemac10$V1) combined_rhemac10_count_matrix_good_cells <- combined_rhemac10_count_m…
Comment: Integration of transcriptomics and proteomics: difficult matching names by ntsopoul ▴ 60
you are right! Excel just did not find it...
Answer: Integration of transcriptomics and proteomics: difficult matching names by ntsopoul ▴ 60
I found a good solution but it is really cumbersome. I use UniProt.ws to derive unique gene names (readable names) and also ambiguous name…
Comment: Merging Outputs from plink --assoc and --hardy to Produce Table by Koketso • 0
Thank you so much. How about calculating allelic odds ratios? Which plink/R command can I use for that?
Comment: Integration of transcriptomics and proteomics: difficult matching names by ATpoint 81k
For such analysis I always first translate everything to Ensembl Gene IDs (biomaRt is a good help here) and then I do the matching with thi…
Comment: Rename multiple fastq.gz files by bk11 ★ 2.3k
Of course! If it worked, accept the answer.
Comment: Integration of transcriptomics and proteomics: difficult matching names by GenoMax 141k
I can see this in the list GI:2387631 Nup42 O Gene nucleoporin 42 10.72 5 24369961 24389011 + AA867018|AB067574|AI426644|AK077066|AK07…
Comment: Rename multiple fastq.gz files by Jérémie • 0
Sorry, I misunderstood. Thank you so much for this.
Comment: Integration of transcriptomics and proteomics: difficult matching names by sansan_96 ▴ 80
Hello, This conversion tool has been useful to me, maybe it can help you: https://biit.cs.ut.ee/gprofiler/convert
Comment: BRAKER3 genome annotation by sansan_96 ▴ 80
Perhaps eggNOG-MAPPER can be useful for functional annotation: 1. https://academic.oup.com/nar/article/47/D1/D309/5173662 2. http://eggnog…
Comment: BRAKER3 genome annotation by Buffo ★ 2.4k
I suggest searching for the difference between structural annotation (identifying the coordinates of the ORFs in a sequence) and functional…
Comment: Integration of transcriptomics and proteomics: difficult matchin names by ntsopoul ▴ 60
looks good but I cannot find either Nupl2 nor Nup42 in the list!
Comment: Integration of transcriptomics and proteomics: difficult matchin names by GenoMax 141k
This table from Jackson labs that correlates many mouse identifiers with external databases will help. Look at the headers of the columns t…
Comment: Rename multiple fastq.gz files by bk11 ★ 2.3k
I just gave hint in the comment above. Please try this, it should work for you. #!/bin/bash for file in `ls *fastq.gz`; do f…
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