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News. Website moved to GitHub.The eXpress website at bio.math.berkeley.edu is now defunct.

• Expression

This GitHub site now serves as the project archive. Note that the eXpress software is also no longer being developed. We recommend you use instead. eXpress Mac 1.5.1 binary updated.The previous 1.5.1 binary for OSX was linked with a dynamic Protobuf library that caused the binary to fail on systems without the library installed.

The binary has now been updated.There is no need to update if you were not using this binary or the binary was working for you previously. eXpress now available in the cloud with!Thanks in major part to the amazing work of, a distributed, batch version of eXpress can now be run on a cluster using to provide a scalable solution for fragment assignment and abundance estimation. Since uses the full batch EM algorithm, it provides the most accurate estimates according to our tests.For more details, please read our in BMC Bioinformatics and check out the on GitHub.

eXpress 1.5.1 releasedThis update is a minor patch containing the following bug fixes:. Fixed occasional crash during writing of results. Added support for FASTA files containing empty lines. eXpress is now on GitHub!In order to speed up development, we're excited to announce that the eXpress codebase will now be stored on a public repository at GitHub.If you have a feature you want to add or a bug you want to fix, please feel free to make a pull request. If you're just interested in helping further the project along but don't have anything specific in mind, check out the page! We always have a few more ideas than we have time to implement.Thanks to everyone for their contributions so far.

We hope you can help make eXpress even better!. eXpress 1.5.0 releasedThis update contains the following fixes and improvements:. Now compatible with inputs containing more than 2 haplotypes. Just create a comma-separate list of haplotypes, one set per line, and use the option.

Thanks to Lindy McBride for helping test this feature. Added TPM to output. Thanks to Richard Smith for the implementation!. Made auxiliary parameter updates atomic to correct biases that are most apparent in ASE analyses. Leads to significant improvements in accuracy even in non-ASE settings. See the for more details. Thanks to William Nelson for helping squash this bug.More exciting news coming later this week.stay tuned!.

eXpress 1.4.1 releasedThis update is a minor patch containing the following bug fixes:. Fixed bug occasionally causing NaNs to appear in output for single-end datasets. Slight correction to likelihood calculation for very short targets. Fixed crash when using -no-error-model. eXpress 1.4.0 releasedMajor Changes:.

Added improved support for allele-specific expression for phased transcripts. See theoption for more details. Improved logging, now using stderr by default. Made bundle handling and merging threadsafe. Added max-read-len option and related error message. Optional compilation using GooglePerfTools TCMalloc for improved speed.

Various minor bug fixes and performance improvements. Sneak peak at eXpress 2We are presenting a poster at ISMB 2013 highlighting the new 'RNA-DNA Difference/RNA Editing'detection feature coming in eXpress 2 this fall. If you aren't at the conference, you canview the poster.

Expression

ReXpress now available!The developers of eXpress along with UC Berkeley MCB graduate student Lorian Schaefferhave developed a new method for updating abundance estimates after a change in the annotation.Details on the method can be found in our recent.The method has been implemented in a software tool called ReXpress, which can be found at. User Forum. eXpress 1.3.1 releasedWe have now created a for users to ask questions, provide assistance, share best practices, and post useful scripts. This is a great first stop if you need help using eXpress!eXpress 1.3.1 Changes:.

Corrected an issue where output SAM/BAM files were partially truncated. Removed a directional (RF) warning that occurred improperly. '/1' and '/2' are now automatically stripped from the suffix of read names.

FPKM is now reported in scientific notation. Online estimates are now rescaled and projected before additional batch rounds. eXpress 1.3.0 releasedChanges:. Fixed an issue where indel parameters were not properly used in the likelihood. Added indel parameters to the params.xprs output file.

Position indexing in params.xrps is now 1-based. Added the ability to load parameters from a params.xprs file. See the -aux-param-file option in for more details. Corrected minor issue that could effect variance bounding. Added -library-size option for FPKM calculations. See the for more details.

Added warning when dataset is too small for computing bias parameters. eXpress 1.2.2 releasedChanges:.

Fixed an issue affecting the variance, which led to unreasonably large confidence intervals and invalid ambiguous count distribution parameters. Theseparameters (alpha and beta) will now always be greater than 0. Fixed an in issue making it impossible to enable additional batch rounds using the -B/-additional-batch option.

Added options for single-end strand-specific protocols ( -f-stranded and -r-stranded). See the for more details. Added a warning message when a library is likely strand-specific but the proper flag has not been given. The beta binomial distribution parameters are now reported in scientific notation in results.xprs. eXpress manuscript now available online!The eXpress manuscript will appear in the January issue of Nature Methods. However, an earlyonline version is now available on the Nature Methods website:Roberts A and Pachter L (2012).Streaming fragment assignment for real-time analysis of sequencing experiments. Nature Methods.→.

eXpress 1.2.1 releasedThis release includes changes to the available options as well as patches for the bugs listed below. Made some previously hidden options available as 'Advanced Options'. See the for more details. Fixed a rare issue affecting indels whereby indels were not properly being penalized in alignment likelihoods. Added a maximum allowed indel size along with geometrically distributed prior on indel length probabilities to correct this issue. See -max-indel-size argument in the for more details. Fixed a bug leading to incorrect learning of mismatch parameters (introduced in 1.2.0).

Fixed a bug leading to a segfault when using single-end reads (introduced in 1.2.0). Added missing CMake configuration file to source tarball.

Dear Customer,when you perform a tracking enquiry and get a result displayed, we are sorry to say that this result table may be difficult to understand if you are using assistive technologies like a screenreader.If you face any problem in reading your tracking results and need assistance, please phone our Express Customer Service at or fill out our. We apologise for any inconvenience and assure you that this issue will be solved quite soon.Please read these result table summary first:The table has a header that informs you about the Waybill tracked and the origin and destination locations of the shipment. The table is intersected by day and date. The first column is a running event ID, the second describes the event, the third indicates the hub location, the fourth gives you the time when the event took place and optionally, a fifth column gives you information on the individual pieces of this shipment.