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737 results • Page
1 of 15
Sort: Votes
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Views
Votes
Replies
362
votes
82
replies
144k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 8 weeks ago by
jena
▴ 290 • written 11.3 years ago by
ole.tange
★ 4.4k
231
votes
38
replies
147k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 11 months ago by
Ram
44k • written 11.2 years ago by
Malachi Griffith
20k
128
votes
83
replies
13k
views
8 follow
Tool:
Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
lossless-fastq-compression
fastq-compressor
updated 11 months ago by
Ram
44k • written 7.1 years ago by
Petr Ponomarenko
★ 2.8k
85
votes
46
replies
9.3k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 10 weeks ago by
LauferVA
4.2k • written 11 months ago by
Sasha
▴ 850
79
votes
86
replies
32k
views
20 follow
Tool:
Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify
storage
bbmap
pigz
compression
updated 11 months ago by
Ram
44k • written 7.5 years ago by
Brian Bushnell
20k
76
votes
14
replies
13k
views
10 follow
Tool:
karyoploteR: uncircle your genomes
karyoploteR
Rdataviz
NGS
updated 11 months ago by
Ram
44k • written 7.0 years ago by
bernatgel
★ 3.4k
72
votes
71
replies
31k
views
17 follow
Tool:
EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot
bioconductor
ggplot2
ggrepel
updated 11 months ago by
Ram
44k • written 5.7 years ago by
Kevin Blighe
88k
68
votes
25
replies
16k
views
12 follow
Tool:
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq
SRA
updated 7 months ago by
GenoMax
142k • written 5.2 years ago by
Phil Ewels
★ 1.4k
61
votes
51
replies
22k
views
9 follow
Tool:
Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files
sff
sequence
fastq
next-gen
updated 11 months ago by
Ram
44k • written 10.1 years ago by
BioApps
▴ 790
56
votes
23
replies
5.2k
views
10 follow
Tool:
ASCIIGenome: Text Only Genome Viewer!
terminal
genome-browser
java
ASCIIGenome
updated 11 months ago by
Ram
44k • written 7.9 years ago by
dariober
14k
56
votes
52
replies
50k
views
12 follow
Tool:
Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF
Gene-Clustering
updated 11 months ago by
Ram
44k • written 9.8 years ago by
EagleEye
7.5k
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 11 months ago by
Ram
44k • written 11.0 years ago by
chbelhumeur2000
▴ 40
54
votes
13
replies
10k
views
6 follow
Tool:
Bedtools: Analyzing Genomic Features
bedtools
updated 11 months ago by
Ram
44k • written 12.1 years ago by
Istvan Albert
100k
53
votes
13
replies
5.7k
views
6 follow
Tool:
I made a DNA/gene/bioinformatics-y workshop for 11-16 year olds which people may find useful
school-outreach
updated 16 months ago by
Ram
44k • written 9.0 years ago by
Daniel
★ 4.0k
53
votes
6
replies
9.8k
views
8 follow
Tool:
list of dockerized bioinformatics apps
docker
updated 2.3 years ago by
Ram
44k • written 9.6 years ago by
14134125465346445
★ 3.6k
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
Ram
44k • written 10.7 years ago by
arnaud.desfeux
▴ 450
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 11 months ago by
Ram
44k • written 6.8 years ago by
sonpham
▴ 580
46
votes
9
replies
43k
views
7 follow
Tool:
Tools to merge overlapping paired-end reads
ngs
Assembly
fastq
updated 13 months ago by
Charles-Alexandre Roy
▴ 50 • written 7.5 years ago by
Abdul Rafay Khan
★ 1.2k
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 11 months ago by
Ram
44k • written 8.1 years ago by
John
13k
38
votes
19
replies
11k
views
Tool:
Excel add-in for DNA/RNA string manipulations
sequence
DNA
RNA
Excel
updated 11 months ago by
Ram
44k • written 8.2 years ago by
jgbaum
▴ 140
34
votes
30
replies
3.0k
views
6 follow
Tool:
BioFlows - Container-enabled Bioinformatics pipeline engine
workflow
next-gen
RNA-Seq
pipeline
updated 14 months ago by
Ram
44k • written 3.4 years ago by
drsami
▴ 90
34
votes
9
replies
11k
views
7 follow
Tool:
Bwa-Meth: Align And Tabulate Bs-Seq Reads
methylation
updated 11 months ago by
Ram
44k • written 10.3 years ago by
brentp
24k
33
votes
3
replies
15k
views
Tool:
Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem
bwa
ngs
updated 11 months ago by
Ram
44k • written 11.2 years ago by
lh3
33k
32
votes
6
replies
12k
views
Tool:
FASTA and FASTQ tools
Cpp
FASTA
Python
FASTQ
updated 16 months ago by
Ram
44k • written 9.0 years ago by
Kamil
★ 2.3k
31
votes
30
replies
15k
views
6 follow
Tool:
BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene
RNA-Seq
Venn-diagram
PCA
updated 11 months ago by
Ram
44k • written 6.0 years ago by
Jennifer Pham
▴ 450
31
votes
22
replies
13k
views
6 follow
Tool:
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
FASTQ
SeqKit
FASTA
updated 11 months ago by
Ram
44k • written 7.6 years ago by
shenwei356
8.5k
30
votes
15
replies
10k
views
7 follow
Tool:
Snakemake--Python-Based Workflow Management
workflow
snakemake
python
updated 11 months ago by
Ram
44k • written 10.5 years ago by
Sean Davis
27k
29
votes
20
replies
3.8k
views
Tool:
FastQt : a clone of FastQC in C++/Qt
fastqc
Cpp
fastq
Qt
updated 11 months ago by
Ram
44k • written 7.5 years ago by
sacha
★ 2.4k
29
votes
29
replies
3.6k
views
6 follow
Tool:
weld (former brew) - yet another fastq utility
illlumina
python
updated 22 months ago by
Ram
44k • written 8.3 years ago by
tinysnippets
▴ 40
28
votes
4
replies
15k
views
Tool:
Plotting GSEA output in R
RNA-Seq
javaGSEA
GSEA
updated 11 months ago by
Ram
44k • written 7.8 years ago by
thomaskuilman
▴ 850
28
votes
17
replies
5.1k
views
7 follow
Tool:
PCAtools: everything Principal Components Analysis
eigenvector
pca
bioconductor
R
updated 11 months ago by
Ram
44k • written 5.3 years ago by
Kevin Blighe
88k
28
votes
7
replies
11k
views
Tool:
Quast Is A Convenient Tool For Assembly Evaluation
assembly
quality
updated 11 months ago by
Ram
44k • written 11.2 years ago by
Nikolay Vyahhi
★ 1.3k
27
votes
12
replies
11k
views
Tool:
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
QC
Trimming
Read
Trimmer
updated 2.6 years ago by
Ram
44k • written 9.9 years ago by
Malachi Griffith
20k
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 11 months ago by
Ram
44k • written 7.8 years ago by
WouterDeCoster
47k
27
votes
5
replies
1.9k
views
6 follow
Tool:
Efficient querying of genomic reference databases with gget
ensembl
enrichr
ncbi
gget
uniprot
updated 24 months ago by
Lior Pachter
▴ 700 • written 24 months ago by
Laura Luebbert
▴ 450
27
votes
6
replies
16k
views
Tool:
Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 11 months ago by
Ram
44k • written 11.9 years ago by
Istvan Albert
100k
26
votes
4
replies
3.3k
views
Tool:
LabWorm - a new CrowdSourcing platform for finding the newest & best bioinformatic tools
LabWorm
updated 13 months ago by
Ram
44k • written 8.0 years ago by
roy.granit
▴ 880
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
Ram
44k • written 7.3 years ago by
Brian Bushnell
20k
26
votes
4
replies
5.3k
views
Tool:
Dgidb - Mining The Druggable Genome
dgidb
drug-gene-interaction
updated 11 months ago by
Ram
44k • written 10.6 years ago by
Obi Griffith
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 11 months ago by
Ram
44k • written 8.0 years ago by
hcwang
▴ 50
25
votes
17
replies
17k
views
Tool:
HeatmapGenerator: High performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C…
heatmap
microarray
R
Cpp
RNA-Seq
updated 2.2 years ago by
Ram
44k • written 9.4 years ago by
Bohdan Khomtchouk
▴ 350
25
votes
3
replies
5.0k
views
Tool:
Quick statistics from the command line
statistics
C
updated 17 months ago by
Ram
44k • written 8.9 years ago by
Kamil
★ 2.3k
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
Ram
44k • written 6.2 years ago by
egeulgen
★ 1.3k
24
votes
26
replies
3.7k
views
Tool:
ClinCNV: CNV detection from short reads
variant-calling
cna
cnv
updated 11 months ago by
Ram
44k • written 4.6 years ago by
German.M.Demidov
★ 2.9k
23
votes
10
replies
12k
views
Tool:
ggtree: phylogenetic tree visualization and annotation
ggtree
phylogeny
visualization
updated 11 months ago by
Ram
44k • written 7.9 years ago by
Guangchuang Yu
★ 2.6k
23
votes
19
replies
4.3k
views
7 follow
Tool:
Big Browser : a new genom browser in development
genome-browser
updated 11 months ago by
Ram
44k • written 8.2 years ago by
sacha
★ 2.4k
22
votes
5
replies
8.4k
views
Tool:
Salmon: A fast and versatile new tool for RNA-seq quantification
RNA-Seq
updated 2.2 years ago by
Ram
44k • written 9.4 years ago by
Rob
6.6k
22
votes
17
replies
4.0k
views
Tool:
epic: new ChIP-Seq caller based on the SICER algorithm
ChIP-Seq
updated 11 months ago by
Ram
44k • written 8.1 years ago by
endrebak
▴ 960
22
votes
8
replies
6.6k
views
Tool:
BioTuring Browser: Making single-cell sequencing data in published studies really accessible!
scRNA-Seq
single-cell
updated 11 months ago by
Ram
44k • written 5.7 years ago by
sonpham
▴ 580
22
votes
4
replies
8.6k
views
Tool:
Very Bad Things
python
text
updated 17 months ago by
Ram
44k • written 11.3 years ago by
brentp
24k
737 results • Page
1 of 15
Recent Votes
A: Fold change - a final explanation
Comment: scRNA-seq quality control
Comment: How to get the ratio of allele counts from GATK derived VCF file?
Setting up Aspera Connect (ascp) on Linux and macOS
Setting up Aspera Connect (ascp) on Linux and macOS
Answer: Genes' fpkm values through cufflink
Answer: Genes' fpkm values through cufflink
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adarsh_pp
▴ 40
Scholar
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LChart
3.9k
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ATpoint
82k
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liyong
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Shicheng Guo
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Recent Replies
Comment: Is it possible to run CibersortX with a very small number of samples?
by
Aspire
▴ 330
Thanks. I have checked that all files are tab delimited, with the first column named Gene_Symbols, with capitalized gene symbols, and no qu…
Answer: samtools write-index
by
aw7
▴ 300
Someone, presumably you, opened an [issue][1] for the same problem. The answer was: > This problem should be fixed in htslib 1.20 (incl…
Answer: How do we do quantification using stringtie merge option for all the merged samp
by
i.sudbery
19k
If you are asking StringTie to estimate expression, then you need to provide it with BAM or CRAM files of the original reads, not a stringt…
Answer: How to interpret this plotMDS of three disease clusters?
by
i.sudbery
19k
> 1) How should I interpret this, can I say that there are practically no differences or outliers? You can say that the inter-group vari…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
emmanouil.a
▴ 120
personaly I see the workstations in long-term ... maybe today you are running only scRNA but having a good workstation tomorrow you can als…
Comment: Z score
by
Akash D
▴ 40
Alright! Got you...
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
i.sudbery
19k
It very much depends on whether the OP does want/need to do the CellRanger runs locally or not. Doesn't really matter if its only occasion…
Comment: log2 fold change in RNA-seq analysis
by
Mensur Dlakic
★ 27k
Everything is already explained on this page, just read everything already written above. Specifically, [**this comment**][1]. [1]: htt…
Comment: log2 fold change in RNA-seq analysis
by
May Ling
• 0
Good day everyone, Sorry I found a bit confusing and would appreciate if I could clarify on the calculation. I am using DESeq. My desire…
Answer: GWAS Phenotypes
by
韩雨
• 0
In my opinion, the basis of the question is to solve whether the phenotype is regulated by genetics. In the aspect of genetic, the estima…
Answer: Classic threshold for log2 fold change in RNA-seq experiment
by
May Ling
• 0
Good day everyone, Sorry I found a bit confusing and would appreciate if I could clarify on the calculation. I am using DESeq. My desire…
Comment: some error in building kraken2 database
by
ahmet
• 0
Were you able to fix this issue? I'm also trying to add external species to krakendb
Comment: Z score
by
ATpoint
82k
logFCs are a bit difficult to cluster I think, because fold changes without stats attached to it are meaningless. They can be very big, due…
Comment: Z score
by
Akash D
▴ 40
Ok. However, if i perform it on log2FC, there wont be any control samples visible in my heatmap. Your answer is perfect.
Comment: Z score
by
ATpoint
82k
You can apply Z-scores on whatever you want, but it must make sense and depends on what you want to do. What is the context? See for exampl…
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