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738 results • Page
2 of 15
Sort: Votes
Rank
Views
Votes
Replies
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
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 8.2 years ago by
endrebak
▴ 960
21
votes
11
replies
11k
views
Tool:
Segemehl: A Fast One-Stop-Shop Mapping Tool
mapping
next-gen
updated 11 months ago by
Ram
44k • written 11.7 years ago by
David Langenberger
11k
21
votes
11
replies
2.8k
views
Tool:
log / log.bio - keeping track of command line workflows
ac.gt
log.bio
log
updated 20 months ago by
Ram
44k • written 8.7 years ago by
John
13k
21
votes
14
replies
9.6k
views
Tool:
trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
visualization
igv
ChIP-Seq
R
bigwigs
updated 11 months ago by
Ram
44k • written 3.5 years ago by
poisonAlien
★ 3.2k
20
votes
23
replies
7.3k
views
6 follow
Tool:
EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
easeq
Windows
Visualization
ChIP-Seq
updated 11 months ago by
Ram
44k • written 8.1 years ago by
Mads Lerdrup
▴ 460
19
votes
2
replies
5.4k
views
Tool:
CIViC - Clinical Interpretation of Variants in Cancer
clinical-interpretation
civic
variant
cancer
updated 11 months ago by
Ram
44k • written 9.2 years ago by
Obi Griffith
20k
19
votes
5
replies
9.0k
views
Tool:
Automatic IGV snapshot script
ChIP-Seq
IGV
updated 14 months ago by
Ram
44k • written 7.2 years ago by
steve
★ 3.5k
19
votes
5
replies
8.0k
views
Tool:
deepTools: user-friendly tools for the normalization and visualization of deep-sequencing data
Visualisation
RNA-Seq
QC
ChIP-Seq
updated 11 months ago by
Ram
44k • written 10.0 years ago by
Björn
▴ 670
19
votes
14
replies
8.3k
views
7 follow
Tool:
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
PolyG
Quality-Control
Filtering
Fastq
AfterQC
updated 11 months ago by
Ram
44k • written 8.1 years ago by
chen
★ 2.5k
19
votes
4
replies
7.7k
views
Tool:
NanoPack: Scripts for long read sequencing data processing and analysis: NanoPlot, NanoFilt, NanoStat, NanoLyse, NanoComp
pacbio
long-reads
oxford-nanopore
updated 11 months ago by
Ram
44k • written 6.7 years ago by
WouterDeCoster
47k
19
votes
9
replies
6.1k
views
Tool:
Rlsim, A Package For Simulating Rna-Seq Library Preparation With Parameter Estimation
simulation
rna-seq
pcr
illumina
updated 11 months ago by
Ram
44k • written 11.1 years ago by
Botond Sipos
★ 1.7k
18
votes
21
replies
4.5k
views
Tool:
uQ - small binary FASTQ
Compression
FASTQ
updated 11 months ago by
Ram
44k • written 7.2 years ago by
John
13k
18
votes
6
replies
4.9k
views
Tool:
R code for ecological data analysis
next-gen
R
Metagenomics
updated 2.2 years ago by
Ram
44k • written 9.4 years ago by
umer.zeeshan.ijaz
★ 1.8k
18
votes
39
replies
4.4k
views
Tool:
CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 12 months ago by
Ram
44k • written 5.1 years ago by
chernouhov sergey
▴ 50
18
votes
30
replies
10k
views
6 follow
Tool:
Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
Illumina
BBMap
filterbytile
updated 11 months ago by
Ram
44k • written 7.4 years ago by
Brian Bushnell
20k
18
votes
22
replies
4.6k
views
Tool:
FAST: FAST Analysis of Sequences Toolbox
NCBI-Taxonomy
pipeline
multiFASTA
BioPerl
updated 23 months ago by
Ram
44k • written 9.1 years ago by
Peter Becich
▴ 70
18
votes
2
replies
6.1k
views
Tool:
vcfanno quickly annotate a vcf with other VCFs, BEDs, BAMs
VCF
variant-annotation
updated 11 months ago by
Ram
44k • written 8.9 years ago by
brentp
24k
18
votes
1
reply
3.5k
views
Tool:
Human NGS Cancer Data for tool development, algorithm benchmarking, teaching, pipeline evaluation, etc.
WGS
Benchmarking
Cancer-Data
updated 19 months ago by
Ram
44k • written 8.8 years ago by
Malachi Griffith
20k
17
votes
11
replies
11k
views
6 follow
Tool:
Pyfaidx: Efficient, "Pythonic" Random Access To Fasta Files Using Samtools-Compatible Indexing
fasta
python
samtools
updated 11 months ago by
Ram
44k • written 10.3 years ago by
Matt Shirley
10k
17
votes
25
replies
2.5k
views
Tool:
Platform for Bioinformatics Students, Scholars and Scientists
sequence
genome
updated 11 months ago by
Ram
44k • written 8.2 years ago by
support
▴ 50
17
votes
9
replies
17k
views
6 follow
Tool:
ggrepel: repel overlapping text labels in ggplot2
R
visualization
updated 11 months ago by
Ram
44k • written 8.4 years ago by
Kamil
★ 2.3k
17
votes
9
replies
6.1k
views
Tool:
Pathomx: Metabolic Pathway Visualisation And Analysis
python
pathway-visualization
updated 11 months ago by
Ram
44k • written 11.1 years ago by
Martin Fitzpatrick
▴ 180
16
votes
3
replies
11k
views
Tool:
Vcflib Documentation
vcf
updated 11 months ago by
Ram
44k • written 11.2 years ago by
Erik Garrison
★ 2.4k
16
votes
16
replies
7.7k
views
6 follow
Tool:
Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data
annotation
fusion
rna-seq
ngs
updated 11 months ago by
Ram
44k • written 10.8 years ago by
mikhail.shugay
3.5k
16
votes
9
replies
8.7k
views
Tool:
Introducing eLabFTW : free open source electronic lab notebook
eln
open-source
notebook-software
updated 2.4 years ago by
Ram
44k • written 9.8 years ago by
Nico
▴ 190
15
votes
8
replies
2.4k
views
Tool:
One Stop Solution for NGS Data Analysis
Predefined Robust NGS Analysis Tool
8.1 years ago by
Persistent LABS
▴ 750
15
votes
2
replies
3.1k
views
Tool:
EnhancedVolcano becomes a pseudo-EnhancedMA
enhancedMA
enhancedvolcano
updated 11 months ago by
Ram
44k • written 3.8 years ago by
Kevin Blighe
88k
15
votes
6
replies
7.2k
views
Tool:
Sambamba: High Performance Alternative For Samtools And Picard For Indexing, Sorting And Merging Bam Files
sambamba
bam
samtools
updated 11 months ago by
Ram
44k • written 10.7 years ago by
William
★ 5.3k
15
votes
19
replies
8.8k
views
6 follow
Tool:
Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations
vcf
database
genome
variation
updated 11 months ago by
Ram
44k • written 11.1 years ago by
Aaronquinlan
12k
15
votes
9
replies
3.4k
views
Tool:
FlexiDot: highly customizable, ambiguity-aware dotplots
dotplot
visualization
sequence-analysis
updated 11 months ago by
Ram
44k • written 6.0 years ago by
toheitka
▴ 230
15
votes
11
replies
8.3k
views
Tool:
Arriba: Fast and accurate gene fusion detection from RNA-Seq data
variant-calling
RNA-Seq
cancer
gene-fusion
updated 11 months ago by
Ram
44k • written 6.3 years ago by
uhrigs
▴ 150
14
votes
4
replies
4.6k
views
Tool:
Seq_File: C Library For Reading Multiple Bioinformatics Sequence File Formats
fasta
fastq
bam
sam
updated 11 months ago by
Ram
44k • written 11.4 years ago by
Jeremy Leipzig
22k
14
votes
10
replies
7.9k
views
Tool:
ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
ReactomePA
R
Visualization
Pathway
Bioconductor
updated 11 months ago by
Ram
44k • written 7.9 years ago by
Guangchuang Yu
★ 2.6k
14
votes
3
replies
4.1k
views
Tool:
Bedops V2.2 Released
bed
updated 11 months ago by
Ram
44k • written 11.1 years ago by
Alex Reynolds
35k
14
votes
4
replies
4.8k
views
Tool:
Revolution (?) in CNA detection using exome/targeted sequencing
copy-number-alteration
next-gen
updated 11 months ago by
Ram
44k • written 9.1 years ago by
Irsan
★ 7.8k
13
votes
14
replies
2.3k
views
Tool:
Collaboration on an empirical QC tool
RNA-Seq
QC
sequencing
updated 11 months ago by
Ram
44k • written 7.0 years ago by
Michael
54k
13
votes
14
replies
6.2k
views
9 follow
Tool:
open-cravat: variant annotation tool
open-cravat
updated 11 months ago by
Ram
44k • written 5.4 years ago by
slcrick
▴ 260
13
votes
6
replies
5.2k
views
Tool:
csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV
Golang
TSV
9 months ago by
shenwei356
8.5k
13
votes
1
reply
4.7k
views
Tool:
sam2pairwise: a tool to visualize SAM entries as pairwise alignments
sam
alignment
updated 2.4 years ago by
Ram
44k • written 9.8 years ago by
Matt LaFave
▴ 310
13
votes
25
replies
11k
views
9 follow
Tool:
Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
analysis
sequencing
ngs
updated 11 months ago by
Ram
44k • written 10.8 years ago by
mikhail.shugay
3.5k
13
votes
2
replies
7.4k
views
Tool:
Software For Detecting Differential Abundance In Meta-Genomic Samples
metagenomics
updated 11 months ago by
Ram
44k • written 11.6 years ago by
Istvan Albert
100k
13
votes
6
replies
4.9k
views
Tool:
GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 11 months ago by
Ram
44k • written 6.8 years ago by
Eric Normandeau
11k
13
votes
6
replies
3.0k
views
Tool:
Open source bioinformatics tools: Blaster, Primer Factory, Labtools
primer
blast
alignment
bowtie
updated 2.4 years ago by
Ram
44k • written 9.4 years ago by
ete
▴ 110
13
votes
7
replies
9.8k
views
Tool:
Command-Line Software For Bigwig Data
bigwig
updated 11 months ago by
Ram
44k • written 10.6 years ago by
andypohl
▴ 90
13
votes
8
replies
4.4k
views
Tool:
MSigDB for Multiple Organisms in a Tidy Data Format
msigdb
pathways
R
gsea
updated 11 months ago by
Ram
44k • written 6.1 years ago by
igor
13k
13
votes
0
replies
2.9k
views
Tool:
Book: GNU Parallel 2018 - for beginners and advanced users
parallel
ngs
updated 11 months ago by
Ram
44k • written 5.6 years ago by
ole.tange
★ 4.4k
13
votes
1
reply
6.6k
views
Tool:
clusterProfiler: an R package for comparing biological themes among gene clusters
GO
clusterProfiler
KEGG
R
GSEA
updated 11 months ago by
Ram
44k • written 7.9 years ago by
Guangchuang Yu
★ 2.6k
13
votes
7
replies
4.2k
views
Tool:
I-PV: a CIRCOS module for interactive protein sequence visualization
interactive
javascript
circos
sequence
updated 21 months ago by
Ram
44k • written 8.6 years ago by
Ibrahim Tanyalcin
★ 1.2k
13
votes
1
reply
3.7k
views
Tool:
Script to compute the effective genome size: epic-effective
ChIP-Seq
updated 11 months ago by
Ram
44k • written 8.1 years ago by
endrebak
▴ 960
738 results • Page
2 of 15
Recent Votes
Answer: Log-transformation, coefficient of variation, standard error and mass-spectromet
Log-transformation, coefficient of variation, standard error and mass-spectrometry based proteomics
Log-transformation, coefficient of variation, standard error and mass-spectrometry based proteomics
Comment: Setting a threshold on gene expression for subsetting (scRNA-seq)
Comment: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
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Recent Replies
Answer: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
jared.andrews07
★ 17k
Go back to your original counts matrix or input data and assign consistent IDs during its generation.
Answer: Facing problem with single cell rna seq annotation using singleR
by
jared.andrews07
★ 17k
A few things. >(1)What did i do wrong here? SingleR will annotate each cell with whatever it's most similar to in the reference datas…
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
Couldn't tell you, I avoid Seurat like the plague.
Comment: What is the best practice of scRNA workflow for multiple patients and samples us
by
Picasa
▴ 640
Same. did you get any solution ?
Comment: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
LauferVA
4.2k
Generally, I cannot advise this in the abstract. The thing is, depending on the treatment group and so forth, there are some transcripts th…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
44k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p
by
Alexandra
• 0
Thank you for your response! Interesting paper.
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
Pierre Lindenbaum
162k
> 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: Harmony integration group.by.var parameter
by
Picasa
▴ 640
@jaredandrews07 If I integrate using Donor: ```R RunHarmony(seu_obj, group.by.vars = c("Donor_ID")) ``` Should I also normalize my data…
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
QX
• 0
thank you so much!
Comment: Attempt to set 'rownames' on an object with no dimensions
by
elbakri.fatimazahrae
• 0
hello everyone, I got the same error for a function immuCellAI_new; result <- ImmuCellAI_new(countData = expr_data_log22, data_type =…
Comment: Merging multiple samples in Seurat
by
Picasa
▴ 640
did you split by sample or donor ?
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
That is correct
Comment: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
ATpoint
82k
That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
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