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12,764 results • Page 3 of 256
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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 6 months ago by 43k • written 14.2 years ago by ★ 1.3k
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing fastq
updated 6 months ago by 161k • written 14.1 years ago by ▴ 660
52
votes
8
replies
60k
views
7 follow
Subsampling Bam File With Samtools
bam samtools
updated 4 months ago by ▴ 10 • written 10.8 years ago by ▴ 250
52
votes
21
replies
49k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 10 months ago by 43k • written 12.1 years ago by ★ 1.5k
52
votes
8
replies
20k
views
6 follow
Fast Interval Intersection Methodologies
genomics
updated 7 months ago by 43k • written 14.2 years ago by ★ 1.0k
51
votes
25
replies
6.9k
views
10 follow
What Is Your Experience With Bioinformatics Webservices?
web-service subjective
updated 6 months ago by 43k • written 14.2 years ago by 54k
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 11 months ago by 43k • written 10.7 years ago by ▴ 450
50
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 7 weeks ago by 100k • written 8.2 years ago by 43k
50
votes
18
replies
36k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq macs ChIP-Seq peaks
updated 10 months ago by 43k • written 7.7 years ago by 13k
50
votes
13
replies
57k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 7 months ago by ▴ 160 • written 8.4 years ago by ▴ 490
49
votes
18
replies
15k
views
12 follow
What Phylogeny Viewing Software Do You Use?
software phylogenetics visualization
updated 6 months ago by 43k • written 14.2 years ago by ▴ 390
49
votes
20
replies
2.1k
views
10 follow
Forum: First experiences matter
first-time tolerance
updated 4 months ago by ★ 2.6k • written 4 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 6 months ago by 43k • written 14.1 years ago by ★ 1.7k
48
votes
14
replies
26k
views
8 follow
Gene Network Construction... Web Based Tool
gene-network
updated 10 months ago by 43k • written 13.0 years ago by ★ 2.8k
48
votes
8
replies
6.8k
views
8 follow
How Far Does Bioinformatics Go?
meta subjective
updated 7 months ago by 43k • written 14.2 years ago by 5.4k
48
votes
9
replies
44k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 3 months ago by ▴ 640 • written 7.5 years ago by ▴ 570
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 10 months ago by 43k • written 6.8 years ago by ▴ 580
48
votes
21
replies
5.1k
views
9 follow
What Online Gene-Centric Resources Do You Use?
gene database
updated 6 months ago by 43k • written 14.1 years ago by 4.9k
47
votes
15
replies
16k
views
10 follow
DESeq2 compare all levels
differential-gene-expression RNA-Seq DESeq2
updated 8 weeks ago by • 0 • written 5.9 years ago by ★ 1.6k
47
votes
26
replies
4.2k
views
11 follow
Blog: Evolution of Biostars
meta Biostars
updated 8 months ago by ▴ 70 • written 5.2 years ago by 7.1k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 9 weeks ago by • 0 • written 3.6 years ago by 3.2k
46
votes
18
replies
10.0k
views
8 follow
Tips To Build A Data Storage For Bioinformatics
data
updated 6 months ago by 43k • written 14.2 years ago by 3.4k
46
votes
14
replies
27k
views
12 follow
Which Bioinformatics Tools Are Written In Python
python
updated 11 months ago by 43k • written 11.8 years ago by ★ 1.1k
45
votes
9
replies
59k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen RNA-Seq single-cell R
updated 9 months ago by ▴ 160 • written 4.5 years ago by ▴ 160
45
votes
4
replies
21k
views
Best way to compare two samples in a VCF file
VCF Variant Genotype Comparison SNP
updated 9 months ago by 43k • written 7.5 years ago by ★ 3.6k
44
votes
9
replies
5.4k
views
6 follow
How Much Do You Trust Geneontology Annotations?
gene-function subjective
updated 7 months ago by 43k • written 14.3 years ago by 28k
43
votes
28
replies
5.6k
views
13 follow
Post Your Prefered Bioinformatics Short Code
code
updated 6 months ago by 43k • written 14.1 years ago by 11k
43
votes
12
replies
5.9k
views
11 follow
What Is The Best Way To Share Scripts Between Members Of A Lab?
general subjective
updated 7 months ago by 43k • written 14.2 years ago by 28k
43
votes
21
replies
5.5k
views
9 follow
Helping Biostar Grow
biostars
updated 6 months ago by 43k • written 14.1 years ago by 11k
43
votes
44
replies
6.1k
views
14 follow
Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?
metagenomics amplicon macbook Intel MacOs
updated 7 months ago by ★ 3.5k • written 7 months ago by ▴ 10
42
votes
16
replies
34k
views
14 follow
Generating consensus sequence from bam file
genome samtools bwa fasta
updated 8 months ago by ★ 1.2k • written 5.2 years ago by ▴ 70
42
votes
15
replies
12k
views
12 follow
Preferred Tools For Making Analysis Pipeline Flowchart ?
pipeline
updated 10 months ago by 43k • written 11.2 years ago by ▴ 730
41
votes
13
replies
26k
views
13 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq DESeq2 geneontology GSEA
updated 9 weeks ago by ▴ 110 • written 6.6 years ago by ▴ 290
40
votes
19
replies
9.7k
views
12 follow
Is There A Site Where Call For Papers And Conferences Are Listed In One Place?
papers conference
updated 6 months ago by 43k • written 14.2 years ago by ▴ 270
40
votes
23
replies
4.2k
views
12 follow
Forum: Why learn programming in bioinformatics?
Programming
updated 11 months ago by 43k • written 5.7 years ago by ▴ 110
40
votes
35
replies
13k
views
10 follow
find positions of a short sequence in a genome
sequence search
updated 9 months ago by ★ 1.5k • written 7.7 years ago by 13k
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 17 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
40
votes
6
replies
15k
views
7 follow
Mapping Ensembl Gene IDs with dot suffix
ensembl gene biomart bioconductor R
updated 9 months ago by 11k • written 6.2 years ago by ▴ 290
39
votes
15
replies
23k
views
9 follow
How Do I Access And Query Entire Genome Sequences With R
gene r
updated 6 months ago by 43k • written 14.2 years ago by ▴ 790
39
votes
21
replies
14k
views
10 follow
Forum: Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 11 months ago by 43k • written 5.6 years ago by 8.6k
39
votes
18
replies
6.1k
views
10 follow
Any Open Notebook Science In Bioinformatics?
open-notebook
updated 6 months ago by 43k • written 14.1 years ago by ▴ 380
39
votes
28
replies
11k
views
10 follow
How Much Does It Cost To Align A Flowcell In The Cloud?
cloud
3 months ago by Jeremy Leipzig 22k
39
votes
16
replies
37k
views
16 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 4 months ago by 142k • written 3.8 years ago by ▴ 160
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 2.8 years ago by ▴ 130
39
votes
11
replies
9.2k
views
11 follow
Where Can I Get The Secondary Structure Of A Protein?
protein structure sequence
updated 7 months ago by 43k • written 14.3 years ago by 28k
38
votes
21
replies
19k
views
8 follow
Tool: pybam - 100% python BAM reader
python htspython bam pysam
updated 11 months ago by 43k • written 8.1 years ago by 13k
38
votes
26
replies
19k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq ChIP-Seq GO gene ontology
written 8.2 years ago by ▴ 370
38
votes
25
replies
9.2k
views
13 follow
FASTA file of fixed length
sequence fasta
updated 8 months ago by 43k • written 8.1 years ago by ▴ 250
38
votes
24
replies
2.2k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 16 days ago by 19k • written 19 days ago by ▴ 580
38
votes
11
replies
4.1k
views
7 follow
Python Documentation Tools
python
updated 11 months ago by 43k • written 14.0 years ago by ★ 3.3k
12,764 results • Page 3 of 256
Recent Votes
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Can I perform a correlation test with 3 biological replicates per condition?
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Comment: API kegg - IndexError: list index out of range by Nyksubuz ▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem by saifulislam99121 • 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite by dario.garvan ▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by GenoMax 142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo. by Ram 43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Ram 43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction by txema.heredia ▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
Comment: Help with VG Toolkit: VCF Output is Empty by Jordan M Eizenga ▴ 460
What do you get if you use `vg stats -a` on the GAM file?
Comment: About runing Pilon on individual chromosomes when polish draft genome assembly by sansan_96 ▴ 90
Hello, What approach could you recommend for a large genome (3Gb) with about 10k scaffolds? I'm having problems with RAM when processing t…
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