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733 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 29 days ago by
jena
▴ 290 • written 11.2 years ago by
ole.tange
★ 4.4k
231
votes
38
replies
146k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Malachi Griffith
19k
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 10 months ago by
Ram
43k • written 7.1 years ago by
Petr Ponomarenko
★ 2.8k
83
votes
46
replies
8.8k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 6 weeks ago by
LauferVA
4.2k • written 10 months ago by
Sasha
▴ 840
79
votes
86
replies
31k
views
20 follow
Tool:
Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify
storage
bbmap
pigz
compression
updated 10 months ago by
Ram
43k • written 7.4 years ago by
Brian Bushnell
20k
76
votes
14
replies
12k
views
10 follow
Tool:
karyoploteR: uncircle your genomes
karyoploteR
Rdataviz
NGS
updated 10 months ago by
Ram
43k • written 6.9 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 10 months ago by
Ram
43k • written 5.6 years ago by
Kevin Blighe
87k
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 6 months ago by
GenoMax
141k • 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 10 months ago by
Ram
43k • written 10.0 years ago by
BioApps
▴ 790
56
votes
52
replies
50k
views
12 follow
Tool:
Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF
Gene-Clustering
updated 10 months ago by
Ram
43k • written 9.7 years ago by
EagleEye
7.5k
56
votes
23
replies
5.0k
views
10 follow
Tool:
ASCIIGenome: Text Only Genome Viewer!
terminal
genome-browser
java
ASCIIGenome
updated 10 months ago by
Ram
43k • written 7.8 years ago by
dariober
14k
54
votes
13
replies
10k
views
6 follow
Tool:
Bedtools: Analyzing Genomic Features
bedtools
updated 10 months ago by
Ram
43k • written 12.0 years ago by
Istvan Albert
100k
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 10 months ago by
Ram
43k • written 10.9 years ago by
chbelhumeur2000
▴ 40
53
votes
13
replies
5.6k
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 15 months ago by
Ram
43k • written 8.9 years ago by
Daniel
★ 4.0k
53
votes
6
replies
9.7k
views
8 follow
Tool:
list of dockerized bioinformatics apps
docker
updated 2.2 years ago by
Ram
43k • written 9.5 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 10 months ago by
Ram
43k • written 10.6 years ago by
arnaud.desfeux
▴ 450
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 10 months ago by
Ram
43k • 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 12 months ago by
Charles-Alexandre Roy
▴ 50 • written 7.4 years ago by
Abdul Rafay Khan
★ 1.2k
38
votes
19
replies
11k
views
Tool:
Excel add-in for DNA/RNA string manipulations
sequence
DNA
RNA
Excel
updated 10 months ago by
Ram
43k • written 8.1 years ago by
jgbaum
▴ 140
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 10 months ago by
Ram
43k • written 8.0 years ago by
John
13k
34
votes
9
replies
11k
views
7 follow
Tool:
Bwa-Meth: Align And Tabulate Bs-Seq Reads
methylation
updated 10 months ago by
Ram
43k • written 10.2 years ago by
brentp
24k
34
votes
30
replies
2.9k
views
6 follow
Tool:
BioFlows - Container-enabled Bioinformatics pipeline engine
workflow
next-gen
RNA-Seq
pipeline
updated 13 months ago by
Ram
43k • written 3.4 years ago by
drsami
▴ 90
33
votes
3
replies
15k
views
Tool:
Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem
bwa
ngs
updated 10 months ago by
Ram
43k • written 11.1 years ago by
lh3
33k
32
votes
6
replies
12k
views
Tool:
FASTA and FASTQ tools
Cpp
FASTA
Python
FASTQ
updated 15 months ago by
Ram
43k • written 8.9 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 10 months ago by
Ram
43k • written 5.9 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 10 months ago by
Ram
43k • written 7.6 years ago by
shenwei356
8.4k
30
votes
15
replies
10k
views
7 follow
Tool:
Snakemake--Python-Based Workflow Management
workflow
snakemake
python
updated 10 months ago by
Ram
43k • written 10.4 years ago by
Sean Davis
26k
29
votes
29
replies
3.5k
views
6 follow
Tool:
weld (former brew) - yet another fastq utility
illlumina
python
updated 21 months ago by
Ram
43k • written 8.2 years ago by
tinysnippets
▴ 40
29
votes
20
replies
3.7k
views
Tool:
FastQt : a clone of FastQC in C++/Qt
fastqc
Cpp
fastq
Qt
updated 10 months ago by
Ram
43k • written 7.4 years ago by
sacha
★ 2.4k
28
votes
4
replies
15k
views
Tool:
Plotting GSEA output in R
RNA-Seq
javaGSEA
GSEA
updated 10 months ago by
Ram
43k • written 7.7 years ago by
thomaskuilman
▴ 850
28
votes
7
replies
11k
views
Tool:
Quast Is A Convenient Tool For Assembly Evaluation
assembly
quality
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Nikolay Vyahhi
★ 1.3k
28
votes
17
replies
5.0k
views
7 follow
Tool:
PCAtools: everything Principal Components Analysis
eigenvector
pca
bioconductor
R
updated 10 months ago by
Ram
43k • written 5.2 years ago by
Kevin Blighe
87k
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 2.5 years ago by
Ram
43k • written 9.9 years ago by
Malachi Griffith
19k
27
votes
6
replies
16k
views
Tool:
Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 10 months ago by
Ram
43k • written 11.8 years ago by
Istvan Albert
100k
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 10 months ago by
Ram
43k • written 7.7 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 23 months ago by
Lior Pachter
▴ 700 • written 23 months ago by
Laura Luebbert
▴ 450
26
votes
22
replies
13k
views
10 follow
Tool:
BBSketch - A Tool for Rapid Sequence Comparison
minhash
sketch
bbmap
blast
updated 11 months ago by
Ram
43k • written 7.2 years ago by
Brian Bushnell
20k
26
votes
4
replies
3.3k
views
Tool:
LabWorm - a new CrowdSourcing platform for finding the newest & best bioinformatic tools
LabWorm
updated 12 months ago by
Ram
43k • written 7.9 years ago by
roy.granit
▴ 880
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 10 months ago by
Ram
43k • written 7.9 years ago by
hcwang
▴ 50
26
votes
4
replies
5.3k
views
Tool:
Dgidb - Mining The Druggable Genome
dgidb
drug-gene-interaction
updated 10 months ago by
Ram
43k • written 10.5 years ago by
Obi Griffith
20k
25
votes
19
replies
8.2k
views
10 follow
Tool:
pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork
R
pathway-enrichment
updated 10 months ago by
Ram
43k • written 6.1 years ago by
egeulgen
★ 1.3k
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 2.1 years ago by
Ram
43k • written 9.3 years ago by
Bohdan Khomtchouk
▴ 350
25
votes
3
replies
4.9k
views
Tool:
Quick statistics from the command line
statistics
C
updated 16 months ago by
Ram
43k • written 8.8 years ago by
Kamil
★ 2.3k
24
votes
26
replies
3.6k
views
Tool:
ClinCNV: CNV detection from short reads
variant-calling
cna
cnv
updated 10 months ago by
Ram
43k • written 4.5 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 10 months ago by
Ram
43k • written 7.8 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 10 months ago by
Ram
43k • written 8.1 years ago by
sacha
★ 2.4k
22
votes
17
replies
3.9k
views
Tool:
epic: new ChIP-Seq caller based on the SICER algorithm
ChIP-Seq
updated 10 months ago by
Ram
43k • written 8.1 years ago by
endrebak
▴ 960
22
votes
20
replies
4.8k
views
Tool:
elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam
bam
bqsr
updated 10 months ago by
Ram
43k • written 5.5 years ago by
Charlotte.Herzeel
▴ 150
22
votes
22
replies
18k
views
Tool:
Pan-Cancer Analysis And Networks Of LncRNAs, MiRNAs, circRNAs, CeRNAs And RNA-Binding Proteins From TCGA 32 Cancer Types and CLIP-seq data
cancer
TCGA
RNA-Binding-Proteins
miRNA
lncRNA
updated 19 months ago by
Ram
43k • written 10.2 years ago by
lsp03yjh
▴ 860
22
votes
4
replies
8.5k
views
Tool:
Very Bad Things
python
text
updated 16 months ago by
Ram
43k • written 11.2 years ago by
brentp
24k
733 results • Page
1 of 15
Recent Votes
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
is oxford nanopore technology data paired or single end sequencing?
is oxford nanopore technology data paired or single end sequencing?
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Hamtaro
▴ 50
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11k
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★ 1.8k
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Recent Replies
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
At this point you should email NCBI help desk and ask them this question. If you get an answer then please post it back in this thread.
Comment: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
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